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  1. data/alias_maps.json +33 -0
  2. data/bacteria_db.xlsx +3 -0
  3. data/extended_proposals.jsonl +138 -0
  4. data/extended_schema.json +201 -0
  5. data/feature_schema.json +86 -0
  6. data/field_weights.json +939 -0
  7. data/gold_tests.json +3 -0
  8. data/llm_gold_examples.json +0 -0
  9. data/rag/index/doc_meta_genus.json +0 -0
  10. data/rag/index/doc_meta_species.json +0 -0
  11. data/rag/index/embedding_genus.npy +3 -0
  12. data/rag/index/embeddings_species.npy +3 -0
  13. data/rag/index/kb_index.json +3 -0
  14. data/rag/knowledge_base/Abiotrophia/defectiva.json +122 -0
  15. data/rag/knowledge_base/Abiotrophia/genus.json +131 -0
  16. data/rag/knowledge_base/Achromobacter/denitrificans.json +99 -0
  17. data/rag/knowledge_base/Achromobacter/genus.json +137 -0
  18. data/rag/knowledge_base/Achromobacter/insolitus.json +95 -0
  19. data/rag/knowledge_base/Achromobacter/xylosoxidans.json +112 -0
  20. data/rag/knowledge_base/Acidaminococcus/fermentans.json +101 -0
  21. data/rag/knowledge_base/Acidaminococcus/genus.json +131 -0
  22. data/rag/knowledge_base/Acidaminococcus/intestini.json +101 -0
  23. data/rag/knowledge_base/Acidovorax/avenae.json +107 -0
  24. data/rag/knowledge_base/Acidovorax/citrulli.json +101 -0
  25. data/rag/knowledge_base/Acidovorax/delafieldii.json +111 -0
  26. data/rag/knowledge_base/Acidovorax/genus.json +133 -0
  27. data/rag/knowledge_base/Acinetobacter/baumannii.json +115 -0
  28. data/rag/knowledge_base/Acinetobacter/calcoaceticus.json +103 -0
  29. data/rag/knowledge_base/Acinetobacter/genus.json +135 -0
  30. data/rag/knowledge_base/Acinetobacter/johnsonii.json +97 -0
  31. data/rag/knowledge_base/Acinetobacter/lwoffii.json +103 -0
  32. data/rag/knowledge_base/Acinetobacter/pittii.json +111 -0
  33. data/rag/knowledge_base/Actinobacillus/actinomycetemcomitans.json +112 -0
  34. data/rag/knowledge_base/Actinobacillus/genus.json +134 -0
  35. data/rag/knowledge_base/Actinobacillus/pleuropneumoniae.json +103 -0
  36. data/rag/knowledge_base/Actinobacillus/suis.json +103 -0
  37. data/rag/knowledge_base/Actinomyces/genus.json +135 -0
  38. data/rag/knowledge_base/Actinomyces/israelii.json +108 -0
  39. data/rag/knowledge_base/Actinomyces/naeslundii.json +106 -0
  40. data/rag/knowledge_base/Actinomyces/odontolyticus.json +106 -0
  41. data/rag/knowledge_base/Aerococcus/genus.json +137 -0
  42. data/rag/knowledge_base/Aerococcus/sanguinicola.json +96 -0
  43. data/rag/knowledge_base/Aerococcus/urinae.json +111 -0
  44. data/rag/knowledge_base/Aerococcus/viridans.json +96 -0
  45. data/rag/knowledge_base/Aeromonas/caviae.json +122 -0
  46. data/rag/knowledge_base/Aeromonas/genus.json +138 -0
  47. data/rag/knowledge_base/Aeromonas/hydrophila.json +122 -0
  48. data/rag/knowledge_base/Aeromonas/veronii.json +122 -0
  49. data/rag/knowledge_base/Aggregatibacter/actinomycetemcomitans.json +108 -0
  50. data/rag/knowledge_base/Aggregatibacter/aphrophilus.json +102 -0
data/alias_maps.json ADDED
@@ -0,0 +1,33 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ {
2
+ "field_aliases": {
3
+ "Dnase": "DNase",
4
+ "CAMP Test": "CAMP",
5
+ "Optochin Sensitivity": "Optochin",
6
+ "Bile Solubility Test": "Bile Solubility",
7
+ "Hippurate": "Hippurate Hydrolysis",
8
+ "PYR Test": "PYR"
9
+ },
10
+ "media_aliases": {
11
+ "mac": "MacConkey Agar",
12
+ "macconkey": "MacConkey Agar",
13
+ "msa": "Mannitol Salt Agar",
14
+ "bap": "Blood Agar",
15
+ "choc": "Chocolate Agar",
16
+ "chocolate": "Chocolate Agar",
17
+ "cled": "CLED Agar"
18
+ },
19
+ "value_aliases_pnv": {
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+ "+": "Positive",
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+ "pos": "Positive",
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+ "positive": "Positive",
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+ "-": "Negative",
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+ "neg": "Negative",
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+ "negative": "Negative",
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+ "variable": "Variable",
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+ "var": "Variable"
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+ },
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+ "Motility": {
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+ "positive": "positive"
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+ }
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+ }
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+ #current ver
data/bacteria_db.xlsx ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:f0a353ee5d5f1488f3d39ed969aa8a112506dc9c59e51e76545fdbb24d9fc881
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+ size 2686741
data/extended_proposals.jsonl ADDED
@@ -0,0 +1,138 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ {"timestamp": "2025-11-16T03:03:53.571998Z", "field_name": "DNase", "freq": 5, "values_seen": {"Positive": 4, "Negative": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573593Z", "field_name": "Lipase", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573653Z", "field_name": "Fermentation Products", "freq": 1, "values_seen": {"Acetic; Butyric": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573685Z", "field_name": "Arginine", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573713Z", "field_name": "NaCl Tolerant (>=15%)", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573739Z", "field_name": "Temperature Dependence", "freq": 1, "values_seen": {"Room Temperature Pigment": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573765Z", "field_name": "NaCl Tolerant (>=10%)", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573791Z", "field_name": "Fermentation Product", "freq": 1, "values_seen": {"Lactic Acid": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573816Z", "field_name": "Arginine Hydrolysis", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573841Z", "field_name": "CAMP Test", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573865Z", "field_name": "Optochin Sensitivity", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573889Z", "field_name": "Other Products", "freq": 1, "values_seen": {"Propionic Acid": 1}}
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+ {"timestamp": "2025-11-16T03:03:53.573913Z", "field_name": "Metabolic Product", "freq": 1, "values_seen": {"Dextran": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.153091Z", "field_name": "DNase", "freq": 142, "values_seen": {"Positive": 52, "Negative": 81, "Variable": 9}}
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+ {"timestamp": "2025-11-24T20:31:45.162359Z", "field_name": "Lipase", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162468Z", "field_name": "Fermentation Products", "freq": 1, "values_seen": {"Acetic; Butyric": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162504Z", "field_name": "Arginine", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162536Z", "field_name": "NaCl Tolerant (>=15%)", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162565Z", "field_name": "Temperature Dependence", "freq": 1, "values_seen": {"Room Temperature Pigment": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162609Z", "field_name": "NaCl Tolerant (>=10%)", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162649Z", "field_name": "Fermentation Product", "freq": 1, "values_seen": {"Lactic Acid": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162728Z", "field_name": "Arginine Hydrolysis", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162778Z", "field_name": "Optochin Sensitivity", "freq": 9, "values_seen": {"Positive": 3, "Negative": 5, "Variable": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162809Z", "field_name": "Other Products", "freq": 1, "values_seen": {"Propionic Acid": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162838Z", "field_name": "Metabolic Product", "freq": 1, "values_seen": {"Dextran": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162867Z", "field_name": "Bacitracin Sensitivity", "freq": 3, "values_seen": {"Positive": 2, "Negative": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.162921Z", "field_name": "Pigment Production", "freq": 160, "values_seen": {"Pyocyanin;Pyoverdine": 1, "Yellow": 75, "Red": 12, "Fluorescent": 2, "Variable": 4, "Brown": 9, "Greenish-yellow": 1, "Yellow;Tan": 2, "Pink": 6, "Black": 5, "Pink;Red": 5, "Fluorescent Green": 1, "Yellow;Yellow-Orange": 1, "Yellow-Green": 5, "Blue-Green": 2, "Negative": 10, "Non-pigmented": 1, "Photochromogenic Yellow": 1, "Orange": 2, "Brown on Bird Seed Agar": 1, "Violet": 1, "Fluorescent Yellow-Green": 1, "Greenish": 1, "Cream": 1, "Yellowish": 1, "Yellow;Orange": 1, "Dark Red": 1, "Pink-Red": 1, "Yellow-Brown": 1, "Pale Pink": 1, "Yellow-White": 2, "Yellow;Cream": 1, "Pale Yellow": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163012Z", "field_name": "Indoxyl Acetate", "freq": 8, "values_seen": {"Positive": 4, "Negative": 4}}
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+ {"timestamp": "2025-11-24T20:31:45.163073Z", "field_name": "Growth Requirements", "freq": 11, "values_seen": {"X Factor;V Factor": 2, "L-cysteine;Iron": 2, "V Factor": 1, "L-cysteine": 1, "Hemin": 1, "X Factor": 1, "Haemin;Vitamin K": 1, "Complex Nutrients": 1, "Hemin;Vitamin K": 1}}
30
+ {"timestamp": "2025-11-24T20:31:45.163126Z", "field_name": "Aerolysin Production", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163175Z", "field_name": "Bile Esculin", "freq": 42, "values_seen": {"Positive": 42}}
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+ {"timestamp": "2025-11-24T20:31:45.163209Z", "field_name": "Arrangement", "freq": 11, "values_seen": {"Cocci": 5, "Tetrads": 2, "Chains": 1, "Diplococci": 3}}
33
+ {"timestamp": "2025-11-24T20:31:45.163239Z", "field_name": "Toxin A", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163265Z", "field_name": "Toxin B", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163296Z", "field_name": "Carbohydrate Utilisation", "freq": 19, "values_seen": {"Negative": 18, "Oxidative": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163327Z", "field_name": "Novobiocin Sensitivity", "freq": 25, "values_seen": {"Negative": 8, "Positive": 17}}
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+ {"timestamp": "2025-11-24T20:31:45.163355Z", "field_name": "Acid-fast Stain", "freq": 3, "values_seen": {"Positive": 3}}
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+ {"timestamp": "2025-11-24T20:31:45.163387Z", "field_name": "Nitrogen Fixation", "freq": 2, "values_seen": {"Positive": 2}}
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+ {"timestamp": "2025-11-24T20:31:45.163414Z", "field_name": "Pseudohyphae", "freq": 2, "values_seen": {"Positive": 2}}
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+ {"timestamp": "2025-11-24T20:31:45.163443Z", "field_name": "Germ Tube", "freq": 31, "values_seen": {"Positive": 8, "Negative": 23}}
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+ {"timestamp": "2025-11-24T20:31:45.163469Z", "field_name": "Budding", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163494Z", "field_name": "Hyphae", "freq": 2, "values_seen": {"Negative": 1, "Septate": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163520Z", "field_name": "Ethanol Production", "freq": 3, "values_seen": {"Positive": 3}}
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+ {"timestamp": "2025-11-24T20:31:45.163545Z", "field_name": "Intracellular Lifestyle", "freq": 4, "values_seen": {"Obligate Intracellular": 3, "Facultative Intracellular": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163570Z", "field_name": "Fermentation Substrate", "freq": 1, "values_seen": {"Amino Acids": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163595Z", "field_name": "Morphology Detail", "freq": 3, "values_seen": {"Branching": 2, "Tapered Ends": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163624Z", "field_name": "Toxin Production", "freq": 13, "values_seen": {"Shiga-like Toxin": 1, "Shiga Toxin": 3, "Tetanospasmin": 1, "Pertussis Toxin": 1, "Cytolysin": 1, "Negative": 1, "Lethal;Hemorrhagic": 1, "Toxin A;Toxin B": 1, "Alpha Toxin": 1, "Botulinum Neurotoxin G": 1, "Toxin A; Toxin B": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163660Z", "field_name": "Organic Acids Production", "freq": 67, "values_seen": {"Acetate;Succinate": 2, "Butyrate": 14, "Butyrate;Acetate": 8, "Acetate;Butyrate": 16, "Short-chain Fatty Acids": 1, "Succinate;Acetate": 1, "Propionate": 6, "Lactate": 2, "Acetate": 5, "Valerate;Butyrate": 1, "Acetate;Butyrate;Lactate": 1, "Propionate;Acetate": 5, "Acetate;Lactate": 2, "Acetate;Ethanol": 1, "Acetate;Formate": 1, "Butyrate;Isopropanol": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163694Z", "field_name": "Butyrate Esterase", "freq": 2, "values_seen": {"Positive": 2}}
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+ {"timestamp": "2025-11-24T20:31:45.163722Z", "field_name": "Dextran Production", "freq": 3, "values_seen": {"Positive": 3}}
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+ {"timestamp": "2025-11-24T20:31:45.163766Z", "field_name": "Denitrification", "freq": 5, "values_seen": {"Positive": 5}}
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+ {"timestamp": "2025-11-24T20:31:45.163819Z", "field_name": "Special Metabolism", "freq": 6, "values_seen": {"Arsenite Oxidation": 1, "Reuterin Production": 1, "1,3-Propanediol Production": 1, "Vitamin B12 Production": 1, "Hydrogen Peroxide Production": 1, "p-Cresol Production": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163853Z", "field_name": "Galactose Fermentation", "freq": 4, "values_seen": {"Positive": 4}}
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+ {"timestamp": "2025-11-24T20:31:45.163890Z", "field_name": "UV Resistance", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163918Z", "field_name": "Nalidixic Acid Resistance", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163963Z", "field_name": "Protease Production", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.163992Z", "field_name": "Aerotolerance", "freq": 4, "values_seen": {"Positive": 4}}
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+ {"timestamp": "2025-11-24T20:31:45.164626Z", "field_name": "Lactate Fermentation", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.164835Z", "field_name": "Inositol Assimilation", "freq": 1, "values_seen": {"Positive": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165038Z", "field_name": "Flagella Type", "freq": 2, "values_seen": {"Axial Filaments": 1, "Polar": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165094Z", "field_name": "Developmental Cycle", "freq": 1, "values_seen": {"Elementary Body;Reticulate Body": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165186Z", "field_name": "Substrate Utilisation", "freq": 4, "values_seen": {"Ferrous Iron;Reduced Sulfur": 1, "Ammonia": 1, "Nitrite": 1, "Methanol;C1 Compounds": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165217Z", "field_name": "pH Preference", "freq": 1, "values_seen": {"Acidophilic": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165242Z", "field_name": "Optimal pH", "freq": 1, "values_seen": {"2–3": 1}}
96
+ {"timestamp": "2025-11-24T20:31:45.165270Z", "field_name": "Product", "freq": 2, "values_seen": {"Nitrite": 1, "Nitrate": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165296Z", "field_name": "Radiation Resistance", "freq": 2, "values_seen": {"High": 2}}
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+ {"timestamp": "2025-11-24T20:31:45.165324Z", "field_name": "Environmental Survival", "freq": 1, "values_seen": {"High": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165364Z", "field_name": "Thermophilic", "freq": 2, "values_seen": {"Positive": 2}}
100
+ {"timestamp": "2025-11-24T20:31:45.165408Z", "field_name": "Cephalothin Sensitivity", "freq": 1, "values_seen": {"Positive": 1}}
101
+ {"timestamp": "2025-11-24T20:31:45.165443Z", "field_name": "Metabolic Products", "freq": 10, "values_seen": {"Butyrate;Acetone;Butanol": 1, "Lactic Acid;Hydrogen Peroxide": 1, "Secondary Bile Acids": 1, "Lactic Acid;Ethanol": 3, "Lactic Acid": 3, "Kefiran": 1}}
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+ {"timestamp": "2025-11-24T20:31:45.165474Z", "field_name": "UV Tolerance", "freq": 1, "values_seen": {"High": 1}}
103
+ {"timestamp": "2025-11-24T20:31:45.165502Z", "field_name": "Heat Resistance", "freq": 2, "values_seen": {"High": 2}}
104
+ {"timestamp": "2025-11-24T20:31:45.165528Z", "field_name": "pH Tolerance", "freq": 4, "values_seen": {"Alkaliphile": 3, "Acidophilic": 1}}
105
+ {"timestamp": "2025-11-24T20:31:45.165554Z", "field_name": "Vitamin B12 Production", "freq": 1, "values_seen": {"Positive": 1}}
106
+ {"timestamp": "2025-11-24T20:31:45.165582Z", "field_name": "Enzyme Production", "freq": 1, "values_seen": {"Amylase": 1}}
107
+ {"timestamp": "2025-11-24T20:31:45.165607Z", "field_name": "Attachment Mechanism", "freq": 1, "values_seen": {"AE Lesions": 1}}
108
+ {"timestamp": "2025-11-24T20:31:45.165637Z", "field_name": "Secondary Metabolites", "freq": 6, "values_seen": {"Siderophores": 1, "Lipopeptides": 2, "Surfactants": 1, "Antimicrobial Peptides": 2}}
109
+ {"timestamp": "2025-11-24T20:31:45.165664Z", "field_name": "Ammonia Production", "freq": 1, "values_seen": {"Positive": 1}}
110
+ {"timestamp": "2025-11-24T20:31:45.165689Z", "field_name": "Bioluminescence", "freq": 2, "values_seen": {"Variable": 1, "Positive": 1}}
111
+ {"timestamp": "2025-11-24T20:31:45.165938Z", "field_name": "Metabolism Type", "freq": 11, "values_seen": {"Homofermentative": 2, "Asaccharolytic": 9}}
112
+ {"timestamp": "2025-11-24T20:31:45.165997Z", "field_name": "Chromium Reduction", "freq": 2, "values_seen": {"Positive": 2}}
113
+ {"timestamp": "2025-11-24T20:31:45.166027Z", "field_name": "Metabolic Capability", "freq": 2, "values_seen": {"Hydrocarbon Degradation": 1, "Agar Degradation": 1}}
114
+ {"timestamp": "2025-11-24T20:31:45.166079Z", "field_name": "Melibiose Fermentation", "freq": 3, "values_seen": {"Positive": 3}}
115
+ {"timestamp": "2025-11-24T20:31:45.166112Z", "field_name": "Growth Requirement", "freq": 16, "values_seen": {"Cysteine;Iron": 8, "X Factor": 2, "V Factor": 5, "X Factor;V Factor": 1}}
116
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117
+ {"timestamp": "2025-11-24T20:31:45.166173Z", "field_name": "Phenylalanine Deamination", "freq": 2, "values_seen": {"Positive": 2}}
118
+ {"timestamp": "2025-11-24T20:31:45.166198Z", "field_name": "Nitrite Reduction", "freq": 3, "values_seen": {"Positive": 3}}
119
+ {"timestamp": "2025-11-24T20:31:45.166241Z", "field_name": "Electron Acceptors", "freq": 7, "values_seen": {"Iron;Manganese": 1, "TMAO": 1, "Iron;TMAO": 1, "Iron": 1, "TMAO;Iron": 2, "Iron;Manganese;TMAO": 1}}
120
+ {"timestamp": "2025-11-24T20:31:45.166278Z", "field_name": "Glycyrrhizin Hydrolysis", "freq": 1, "values_seen": {"Positive": 1}}
121
+ {"timestamp": "2025-11-24T20:31:45.166305Z", "field_name": "Pyrazinamidase", "freq": 1, "values_seen": {"Positive": 1}}
122
+ {"timestamp": "2025-11-24T20:31:45.166332Z", "field_name": "Aromatic Compound Degradation", "freq": 1, "values_seen": {"Positive": 1}}
123
+ {"timestamp": "2025-11-24T20:31:45.166359Z", "field_name": "Xylose Oxidation", "freq": 2, "values_seen": {"Positive": 2}}
124
+ {"timestamp": "2025-11-24T20:31:45.166383Z", "field_name": "Blood Agar Growth", "freq": 1, "values_seen": {"Negative": 1}}
125
+ {"timestamp": "2025-11-24T20:31:45.166408Z", "field_name": "Beta-lactamase", "freq": 1, "values_seen": {"Negative": 1}}
126
+ {"timestamp": "2025-11-24T20:31:45.166433Z", "field_name": "Mannitol Oxidation", "freq": 1, "values_seen": {"Positive": 1}}
127
+ {"timestamp": "2025-11-24T20:31:45.166478Z", "field_name": "Colony Odour", "freq": 4, "values_seen": {"Horse Stable": 1, "Citrus": 1, "Grape-like": 1, "Horse-stable": 1}}
128
+ {"timestamp": "2025-11-24T20:31:45.166512Z", "field_name": "Parasporal Crystal", "freq": 1, "values_seen": {"Present": 1}}
129
+ {"timestamp": "2025-11-24T20:31:45.166542Z", "field_name": "Lancefield Group", "freq": 3, "values_seen": {"D": 1, "C or G": 1, "E": 1}}
130
+ {"timestamp": "2025-11-24T20:31:45.166568Z", "field_name": "NaCl Requirement", "freq": 1, "values_seen": {"Positive": 1}}
131
+ {"timestamp": "2025-11-24T20:31:45.166593Z", "field_name": "Fermentation Type", "freq": 1, "values_seen": {"Heterofermentative": 1}}
132
+ {"timestamp": "2025-11-24T20:31:45.166620Z", "field_name": "Ribose Fermentation", "freq": 4, "values_seen": {"Positive": 4}}
133
+ {"timestamp": "2025-11-24T20:31:45.166654Z", "field_name": "Chlamydospore Production", "freq": 21, "values_seen": {"Positive": 6, "Negative": 15}}
134
+ {"timestamp": "2025-11-24T20:31:45.166686Z", "field_name": "Phenol Oxidase", "freq": 7, "values_seen": {"Positive": 7}}
135
+ {"timestamp": "2025-11-24T20:31:45.166714Z", "field_name": "Acid-Fast", "freq": 20, "values_seen": {"Positive": 20}}
136
+ {"timestamp": "2025-11-24T20:31:45.166740Z", "field_name": "Raffinase Fermentation", "freq": 1, "values_seen": {"Negative": 1}}
137
+ {"timestamp": "2025-11-24T20:31:45.166765Z", "field_name": "Inositot Fermentation", "freq": 1, "values_seen": {"Negative": 1}}
138
+ {"timestamp": "2025-11-24T20:31:45.166790Z", "field_name": "Inditol", "freq": 1, "values_seen": {"Negative": 1}}
data/extended_schema.json ADDED
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1
+ {
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+ "CAMP": {
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+ "value_type": "enum_PNV",
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+ "aliases": ["camp test", "camp reaction"]
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+ },
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+
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+ "PYR": {
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+ "value_type": "enum_PNV",
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+ "aliases": ["pyr test", "pyr activity"]
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+ },
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+
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+ "Bile Solubility": {
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+ "value_type": "enum_PNV",
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+ "aliases": ["bile soluble"]
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+ },
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+
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+ "Hippurate Hydrolysis": {
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+ "value_type": "enum_PNV",
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+ "aliases": ["hippurate", "hippurate test"]
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+ },
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+
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+ "Gas Production": {
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+ "value_type": "enum_PNV",
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+ "aliases": [
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+ "gas production",
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+ "gas-producing",
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+ "gas producing",
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+ "gas producer",
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+ "produces gas",
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+ "with gas",
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+ "gas is produced"
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+ ]
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+ },
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+
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+ "Glucose Oxidation": {
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+ "value_type": "enum_PNV",
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+ "aliases": [
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+ "oxidises glucose",
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+ "oxidizes glucose",
40
+ "oxidation of glucose",
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+ "glucose oxidation",
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+ "glucose oxidiser",
43
+ "glucose oxidizer"
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+ ]
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+ },
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+
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+ "Antibiotic Resistance": {
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+ "value_type": "enum_PNV",
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+ "aliases": [
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+ "resistant to",
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+ "antibiotic resistance",
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+ "antibiotic-resistant"
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+ ]
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+ },
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+
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+ "Pigment": {
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+ "value_type": "enum_custom",
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+ "allowed": [
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+ "Blue-Green",
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+ "Green",
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+ "Yellow",
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+ "Red",
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+ "Brown",
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+ "Pink",
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+ "Orange",
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+ "Black",
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+ "Violet"
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+ ],
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+ "blue-green pigment",
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+ "orange pigment",
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+ "black pigment",
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+ "violet pigment",
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+ "pyocyanin",
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+ "pyoverdine",
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+ "pigment production"
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+ ]
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+ },
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+
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+ "Odor": {
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+ "value_type": "enum_custom",
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+ "allowed": [
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+ "Grape",
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+ "Fruity",
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+ "Musty",
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+ "Pungent",
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+ "Putrid",
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+ "Buttery",
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+ "Earthy",
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+ "Mousy",
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+ "Fishy",
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+ "Almond",
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+ "Cheese"
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+ ],
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+ "aliases": [
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+ "grape-like odor",
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+ "fruity odor",
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+ "musty odor",
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+ "pungent odor",
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+ "putrid odor",
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+ "buttery odor",
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+ "earthy odor",
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+ "mousy odor",
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+ "fishy odor",
110
+ "almond odor",
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+ "cheese odor",
112
+ "distinct odor",
113
+ "characteristic smell"
114
+ ]
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+ },
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+
117
+ "Colony Pattern": {
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+ "value_type": "enum_custom",
119
+ "allowed": [
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+ "CIN Bullseye",
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+ "XLD Black Center",
122
+ "Mucoid",
123
+ "Swarming",
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+ "Metallic",
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+ "Smooth",
126
+ "Rough",
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+ "Chalky",
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+ "Filamentous",
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+ "Irregular",
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+ "Corroding",
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+ "Sticky",
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+ "Molar-tooth"
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+ ],
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+ "aliases": [
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+ "cin bullseye colonies",
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+ "bullseye colonies",
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+ "xld black-centered colonies",
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+ "black-centered colonies",
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+ "mucoid colonies",
140
+ "swarming colonies",
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+ "metallic sheen colonies",
142
+ "smooth colonies",
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+ "rough colonies",
144
+ "chalky colonies",
145
+ "filamentous colonies",
146
+ "irregular colonies",
147
+ "corroding colonies",
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+ "sticky colonies",
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+ "molar-tooth colonies"
150
+ ]
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+ },
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+
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+ "Motility Type": {
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+ "value_type": "enum_custom",
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+ "allowed": [
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+ "Tumbling",
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+ "Darting",
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+ "Swarming",
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+ "Umbrella",
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+ "Gliding",
161
+ "Axial",
162
+ "Peritrichous",
163
+ "Polar",
164
+ "Monotrichous",
165
+ "Lophotrichous"
166
+ ],
167
+ "aliases": [
168
+ "tumbling motility",
169
+ "darting motility",
170
+ "swarming motility",
171
+ "umbrella motility",
172
+ "gliding motility",
173
+ "axial filament",
174
+ "peritrichous flagella",
175
+ "polar flagella",
176
+ "monotrichous flagella",
177
+ "lophotrichous flagella"
178
+ ]
179
+ },
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+
181
+ "TSI Pattern": {
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+ "value_type": "enum_custom",
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+ "allowed": [
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+ "A/A",
185
+ "K/A",
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+ "K/K",
187
+ "A/A + Gas",
188
+ "K/A + H2S"
189
+ ],
190
+ "aliases": [
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+ "tsi",
192
+ "tsi reaction",
193
+ "triple sugar iron",
194
+ "a slash a",
195
+ "k slash a",
196
+ "k slash k",
197
+ "h2s production on tsi",
198
+ "gas production on tsi"
199
+ ]
200
+ }
201
+ }
data/feature_schema.json ADDED
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+ {
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+ "version": 2,
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+ "description": "Optimized ML feature schema for genus-level identification.",
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+ "features": [
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+ {"name": "Gram Stain", "kind": "pnv"},
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+ {"name": "Shape", "kind": "shape"},
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+ {"name": "Haemolysis Type", "kind": "pnv"},
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+ {"name": "Oxidase", "kind": "pnv"},
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+ {"name": "Indole", "kind": "pnv"},
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+ {"name": "Urease", "kind": "pnv"},
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+ {"name": "Citrate", "kind": "pnv"},
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+ {"name": "H2S", "kind": "pnv"},
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+ {"name": "DNase", "kind": "pnv"},
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+ {"name": "Lysine Decarboxylase", "kind": "pnv"},
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+ {"name": "Ornithine Decarboxylase", "kind": "pnv"},
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+ {"name": "Arginine dihydrolase", "kind": "pnv"},
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+ {"name": "ONPG", "kind": "pnv"},
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+ {"name": "Nitrate Reduction", "kind": "pnv"},
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+ {"name": "Methyl Red", "kind": "pnv"},
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+ {"name": "VP", "kind": "pnv"},
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+ {"name": "Coagulase", "kind": "pnv"},
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+ {"name": "Lipase Test", "kind": "pnv"},
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+
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+ {"name": "Motility", "kind": "pnv"},
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+ {"name": "Motility Type", "kind": "category"},
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+
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+ {"name": "Capsule", "kind": "pnv"},
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+ {"name": "Spore Formation", "kind": "pnv"},
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+ {"name": "Pigment", "kind": "category"},
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+ {"name": "Odor", "kind": "category"},
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+ {"name": "Colony Pattern", "kind": "category"},
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+
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+ {"name": "TSI Pattern", "kind": "category"},
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+
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+ {"name": "Temperature_4C", "kind": "binary"},
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+ {"name": "Temperature_25C", "kind": "binary"},
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+ {"name": "Temperature_30C", "kind": "binary"},
40
+ {"name": "Temperature_37C", "kind": "binary"},
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+ {"name": "Temperature_42C", "kind": "binary"},
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+
43
+ {"name": "Lactose Fermentation", "kind": "pnv"},
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+ {"name": "Glucose Fermentation", "kind": "pnv"},
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+ {"name": "Sucrose Fermentation", "kind": "pnv"},
46
+ {"name": "Mannitol Fermentation", "kind": "pnv"},
47
+ {"name": "Maltose Fermentation", "kind": "pnv"},
48
+ {"name": "Sorbitol Fermentation", "kind": "pnv"},
49
+ {"name": "Xylose Fermentation", "kind": "pnv"},
50
+ {"name": "Rhamnose Fermentation", "kind": "pnv"},
51
+ {"name": "Arabinose Fermentation", "kind": "pnv"},
52
+ {"name": "Raffinose Fermentation", "kind": "pnv"},
53
+ {"name": "Trehalose Fermentation", "kind": "pnv"},
54
+ {"name": "Inositol Fermentation", "kind": "pnv"},
55
+
56
+ {"name": "Oxygen Requirement", "kind": "oxygen"},
57
+ {"name": "Gas Production", "kind": "pnv"},
58
+
59
+ {"name": "MacConkey Growth", "kind": "media_flag"},
60
+ {"name": "Blood Growth", "kind": "media_flag"},
61
+ {"name": "XLD Growth", "kind": "media_flag"},
62
+ {"name": "Nutrient Growth", "kind": "media_flag"},
63
+ {"name": "Cetrimide Growth", "kind": "media_flag"},
64
+ {"name": "BCYE Growth", "kind": "media_flag"},
65
+ {"name": "Hektoen Enteric Growth", "kind": "media_flag"},
66
+ {"name": "Mannitol Salt Growth", "kind": "media_flag"},
67
+ {"name": "Bordet-Gengou Growth", "kind": "media_flag"},
68
+ {"name": "Thayer Martin Growth", "kind": "media_flag"},
69
+ {"name": "Cycloserine Cefoxitin Fructose Growth", "kind": "media_flag"},
70
+ {"name": "Sabouraud Growth", "kind": "media_flag"},
71
+ {"name": "Lowenstein-Jensen Growth", "kind": "media_flag"},
72
+ {"name": "Yeast Extract Mannitol Growth", "kind": "media_flag"},
73
+ {"name": "BSK Growth", "kind": "media_flag"},
74
+ {"name": "Brucella Growth", "kind": "media_flag"},
75
+ {"name": "Charcoal Growth", "kind": "media_flag"},
76
+ {"name": "BHI Growth", "kind": "media_flag"},
77
+ {"name": "Ashby Growth", "kind": "media_flag"},
78
+ {"name": "MRS Growth", "kind": "media_flag"},
79
+ {"name": "Anaerobic Blood Growth", "kind": "media_flag"},
80
+ {"name": "BP Growth", "kind": "media_flag"},
81
+ {"name": "ALOA Growth", "kind": "media_flag"},
82
+ {"name": "Anaerobic Growth", "kind": "media_flag"},
83
+ {"name": "Chocolate Growth", "kind": "media_flag"},
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+ {"name": "TCBS Growth", "kind": "media_flag"}
85
+ ]
86
+ }
data/field_weights.json ADDED
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+ "short": "Achromobacter denitrificans is a Gram-negative, aerobic, non-fermenting rod characterized by strong nitrate reduction and denitrification capability.",
9
+ "clinical_context": "Rarely associated with human infection and more commonly encountered in environmental samples."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Smooth",
25
+ "Grey"
26
+ ],
27
+ "Oxygen Requirement": "Aerobic",
28
+ "Growth Temperature": "20//37",
29
+ "Catalase": "Positive",
30
+ "Oxidase": "Positive",
31
+ "Indole": "Negative",
32
+ "Urease": "Negative",
33
+ "Citrate": "Variable",
34
+ "Methyl Red": "Negative",
35
+ "VP": "Negative",
36
+ "H2S": "Negative",
37
+ "DNase": "Negative",
38
+ "ONPG": "Negative",
39
+ "Coagulase": "Negative",
40
+ "Gelatin Hydrolysis": "Negative",
41
+ "Esculin Hydrolysis": "Negative",
42
+ "Nitrate Reduction": "Positive",
43
+ "NaCl Tolerant (>=6%)": "Negative",
44
+ "Lipase Test": "Negative",
45
+ "Lysine Decarboxylase": "Negative",
46
+ "Ornithine Decarboxylase": "Negative",
47
+ "Ornitihine Decarboxylase": "Negative",
48
+ "Arginine dihydrolase": "Positive",
49
+ "Glucose Fermentation": "Negative",
50
+ "Lactose Fermentation": "Negative",
51
+ "Sucrose Fermentation": "Negative",
52
+ "Maltose Fermentation": "Negative",
53
+ "Mannitol Fermentation": "Negative",
54
+ "Sorbitol Fermentation": "Negative",
55
+ "Xylose Fermentation": "Negative",
56
+ "Rhamnose Fermentation": "Negative",
57
+ "Arabinose Fermentation": "Negative",
58
+ "Raffinose Fermentation": "Negative",
59
+ "Trehalose Fermentation": "Negative",
60
+ "Inositol Fermentation": "Negative",
61
+ "Gas Production": "Negative",
62
+ "TSI Pattern": "K/K",
63
+ "Colony Pattern": "Unknown",
64
+ "Pigment": "None",
65
+ "Motility Type": "Polar"
66
+ },
67
+
68
+ "species_markers": [
69
+ {
70
+ "field": "Nitrate Reduction",
71
+ "value": "Positive",
72
+ "importance": "high",
73
+ "notes": "Denitrification capability is characteristic of A. denitrificans."
74
+ }
75
+ ],
76
+
77
+ "common_confusions": [
78
+ {
79
+ "species": "Achromobacter xylosoxidans",
80
+ "reason": "Shared oxidase positivity and non-fermentative metabolism."
81
+ }
82
+ ],
83
+
84
+ "when_to_question_identification": [
85
+ "Absence of nitrate reduction argues against A. denitrificans.",
86
+ "Clinical isolation should prompt confirmation due to rarity."
87
+ ],
88
+
89
+ "recommended_next_tests": [
90
+ {
91
+ "test": "Nitrate reduction and denitrification testing",
92
+ "reason": "Defining feature of this species."
93
+ },
94
+ {
95
+ "test": "MALDI-TOF MS",
96
+ "reason": "Required for reliable species-level identification."
97
+ }
98
+ ]
99
+ }
data/rag/knowledge_base/Achromobacter/genus.json ADDED
@@ -0,0 +1,137 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Achromobacter",
5
+
6
+ "overview": {
7
+ "short": "Achromobacter species are Gram-negative, non-fermenting rods commonly found in aqueous environments and occasionally isolated from clinical specimens.",
8
+ "clinical_context": "Most frequently associated with respiratory infections, particularly in patients with cystic fibrosis, as well as opportunistic bloodstream and device-associated infections."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Negative",
13
+ "Shape": "Rods",
14
+ "Motility": "Positive",
15
+ "Capsule": "Unknown",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Negative",
18
+ "Haemolysis Type": "None",
19
+ "Media Grown On": [
20
+ "Blood Agar",
21
+ "MacConkey Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Smooth",
25
+ "Grey",
26
+ "Non-lactose fermenting"
27
+ ],
28
+ "Oxygen Requirement": "Aerobic",
29
+ "Growth Temperature": "20//37",
30
+ "Catalase": "Positive",
31
+ "Oxidase": "Positive",
32
+ "Indole": "Negative",
33
+ "Urease": "Variable",
34
+ "Citrate": "Variable",
35
+ "Methyl Red": "Negative",
36
+ "VP": "Negative",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Negative",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Variable",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Variable",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Negative",
47
+ "Ornithine Decarboxylase": "Negative",
48
+ "Ornitihine Decarboxylase": "Negative",
49
+ "Arginine dihydrolase": "Positive",
50
+ "Glucose Fermentation": "Negative",
51
+ "Lactose Fermentation": "Negative",
52
+ "Sucrose Fermentation": "Negative",
53
+ "Maltose Fermentation": "Negative",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Negative",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Negative",
60
+ "Trehalose Fermentation": "Negative",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "K/K",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "Polar"
67
+ },
68
+
69
+ "field_notes": {
70
+ "Glucose Fermentation": "Achromobacter species are non-fermenters and do not acidify carbohydrates.",
71
+ "Arginine dihydrolase": "Typically positive and a useful discriminator among non-fermenting Gram-negative rods.",
72
+ "Oxidase": "Oxidase positivity helps distinguish Achromobacter from Stenotrophomonas."
73
+ },
74
+
75
+ "key_differentiators": [
76
+ {
77
+ "field": "Oxidase",
78
+ "expected": "Positive",
79
+ "distinguishes_from": ["Stenotrophomonas"],
80
+ "notes": "Oxidase positivity separates Achromobacter from oxidase-negative non-fermenters."
81
+ },
82
+ {
83
+ "field": "Arginine dihydrolase",
84
+ "expected": "Positive",
85
+ "distinguishes_from": ["Pseudomonas"],
86
+ "notes": "Arginine positivity helps differentiate from many Pseudomonas species."
87
+ },
88
+ {
89
+ "field": "Glucose Fermentation",
90
+ "expected": "Negative",
91
+ "distinguishes_from": ["Enterobacter", "Burkholderia"],
92
+ "notes": "Non-fermentative metabolism excludes Enterobacterales."
93
+ }
94
+ ],
95
+
96
+ "common_confusions": [
97
+ {
98
+ "genus": "Pseudomonas",
99
+ "reason": "Shared oxidase positivity and non-fermentative metabolism."
100
+ },
101
+ {
102
+ "genus": "Burkholderia",
103
+ "reason": "Overlap in non-fermenting biochemical profiles and environmental origin."
104
+ },
105
+ {
106
+ "genus": "Stenotrophomonas",
107
+ "reason": "Similar colony morphology on non-selective media."
108
+ }
109
+ ],
110
+
111
+ "when_to_question_identification": [
112
+ "Oxidase-negative isolate suggests Stenotrophomonas.",
113
+ "Strong pigment production suggests Pseudomonas.",
114
+ "Fermentative carbohydrate reactions argue against Achromobacter."
115
+ ],
116
+
117
+ "recommended_next_tests": [
118
+ {
119
+ "test": "Arginine dihydrolase",
120
+ "reason": "Key biochemical marker for Achromobacter identification."
121
+ },
122
+ {
123
+ "test": "Oxidative-fermentative (OF) glucose test",
124
+ "reason": "Confirms non-fermentative metabolism."
125
+ },
126
+ {
127
+ "test": "MALDI-TOF MS",
128
+ "reason": "Recommended due to overlap with other non-fermenting Gram-negative rods."
129
+ }
130
+ ],
131
+
132
+ "supported_species": [
133
+ "xylosoxidans",
134
+ "ruhlandii",
135
+ "insolitus"
136
+ ]
137
+ }
data/rag/knowledge_base/Achromobacter/insolitus.json ADDED
@@ -0,0 +1,95 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Achromobacter",
5
+ "species": "insolitus",
6
+
7
+ "overview": {
8
+ "short": "Achromobacter insolitus is a rarely isolated non-fermenting Gram-negative rod primarily recovered from environmental and occasional clinical sources.",
9
+ "clinical_context": "Uncommonly associated with human infection and usually identified through molecular or mass spectrometry methods."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Smooth",
25
+ "Grey"
26
+ ],
27
+ "Oxygen Requirement": "Aerobic",
28
+ "Growth Temperature": "20//37",
29
+ "Catalase": "Positive",
30
+ "Oxidase": "Positive",
31
+ "Indole": "Negative",
32
+ "Urease": "Variable",
33
+ "Citrate": "Variable",
34
+ "Methyl Red": "Negative",
35
+ "VP": "Negative",
36
+ "H2S": "Negative",
37
+ "DNase": "Negative",
38
+ "ONPG": "Negative",
39
+ "Coagulase": "Negative",
40
+ "Gelatin Hydrolysis": "Variable",
41
+ "Esculin Hydrolysis": "Negative",
42
+ "Nitrate Reduction": "Negative",
43
+ "NaCl Tolerant (>=6%)": "Negative",
44
+ "Lipase Test": "Negative",
45
+ "Lysine Decarboxylase": "Negative",
46
+ "Ornithine Decarboxylase": "Negative",
47
+ "Ornitihine Decarboxylase": "Negative",
48
+ "Arginine dihydrolase": "Positive",
49
+ "Glucose Fermentation": "Negative",
50
+ "Lactose Fermentation": "Negative",
51
+ "Sucrose Fermentation": "Negative",
52
+ "Maltose Fermentation": "Negative",
53
+ "Mannitol Fermentation": "Negative",
54
+ "Sorbitol Fermentation": "Negative",
55
+ "Xylose Fermentation": "Negative",
56
+ "Rhamnose Fermentation": "Negative",
57
+ "Arabinose Fermentation": "Negative",
58
+ "Raffinose Fermentation": "Negative",
59
+ "Trehalose Fermentation": "Negative",
60
+ "Inositol Fermentation": "Negative",
61
+ "Gas Production": "Negative",
62
+ "TSI Pattern": "K/K",
63
+ "Colony Pattern": "Unknown",
64
+ "Pigment": "None",
65
+ "Motility Type": "Polar"
66
+ },
67
+
68
+ "species_markers": [
69
+ {
70
+ "field": "Nitrate Reduction",
71
+ "value": "Negative",
72
+ "importance": "medium",
73
+ "notes": "Helps separate A. insolitus from A. xylosoxidans."
74
+ }
75
+ ],
76
+
77
+ "common_confusions": [
78
+ {
79
+ "species": "Achromobacter xylosoxidans",
80
+ "reason": "Highly similar biochemical profile."
81
+ }
82
+ ],
83
+
84
+ "when_to_question_identification": [
85
+ "Nitrate positivity favors A. xylosoxidans.",
86
+ "Unusual growth patterns warrant molecular confirmation."
87
+ ],
88
+
89
+ "recommended_next_tests": [
90
+ {
91
+ "test": "MALDI-TOF MS",
92
+ "reason": "Necessary for confident species-level identification."
93
+ }
94
+ ]
95
+ }
data/rag/knowledge_base/Achromobacter/xylosoxidans.json ADDED
@@ -0,0 +1,112 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Achromobacter",
5
+ "species": "xylosoxidans",
6
+
7
+ "overview": {
8
+ "short": "Achromobacter xylosoxidans is a Gram-negative, aerobic, non-fermenting rod and the most commonly isolated species of the genus in clinical microbiology.",
9
+ "clinical_context": "Frequently associated with respiratory infections in cystic fibrosis patients, as well as bloodstream and device-associated infections."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Non-lactose fermenting"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "20//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Positive",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Arginine dihydrolase",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Key defining feature of A. xylosoxidans among non-fermenting Gram-negative rods."
76
+ },
77
+ {
78
+ "field": "Nitrate Reduction",
79
+ "value": "Positive",
80
+ "importance": "medium",
81
+ "notes": "Supports differentiation from closely related Achromobacter species."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "genus": "Pseudomonas",
88
+ "reason": "Shared oxidase positivity and non-fermentative metabolism."
89
+ },
90
+ {
91
+ "genus": "Burkholderia",
92
+ "reason": "Overlap in biochemical profile and environmental association."
93
+ }
94
+ ],
95
+
96
+ "when_to_question_identification": [
97
+ "Oxidase-negative result argues against Achromobacter.",
98
+ "Carbohydrate fermentation suggests Enterobacterales.",
99
+ "Pigment production suggests Pseudomonas."
100
+ ],
101
+
102
+ "recommended_next_tests": [
103
+ {
104
+ "test": "Arginine dihydrolase",
105
+ "reason": "Confirms Achromobacter lineage."
106
+ },
107
+ {
108
+ "test": "MALDI-TOF MS",
109
+ "reason": "Gold standard for non-fermenter species differentiation."
110
+ }
111
+ ]
112
+ }
data/rag/knowledge_base/Acidaminococcus/fermentans.json ADDED
@@ -0,0 +1,101 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acidaminococcus",
5
+ "species": "fermentans",
6
+
7
+ "overview": {
8
+ "short": "Acidaminococcus fermentans is a Gram-negative, obligately anaerobic coccus that derives energy primarily from amino acid fermentation.",
9
+ "clinical_context": "Commonly part of the normal gastrointestinal microbiota and occasionally recovered from polymicrobial anaerobic infections."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Cocci",
15
+ "Motility": "Negative",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Small",
25
+ "Grey",
26
+ "Convex"
27
+ ],
28
+ "Oxygen Requirement": "Obligate Anaerobe",
29
+ "Growth Temperature": "35//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Negative",
33
+ "Urease": "Negative",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Negative",
36
+ "VP": "Negative",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Negative",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Negative",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Negative",
47
+ "Ornithine Decarboxylase": "Negative",
48
+ "Ornitihine Decarboxylase": "Negative",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Negative",
51
+ "Lactose Fermentation": "Negative",
52
+ "Sucrose Fermentation": "Negative",
53
+ "Maltose Fermentation": "Negative",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Negative",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Negative",
60
+ "Trehalose Fermentation": "Negative",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "K/K",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Amino Acid Fermentation",
72
+ "value": "Positive",
73
+ "importance": "high",
74
+ "notes": "Primary metabolic pathway distinguishing Acidaminococcus species."
75
+ }
76
+ ],
77
+
78
+ "common_confusions": [
79
+ {
80
+ "genus": "Veillonella",
81
+ "reason": "Both are anaerobic Gram-negative cocci isolated from similar sites."
82
+ }
83
+ ],
84
+
85
+ "when_to_question_identification": [
86
+ "Carbohydrate fermentation suggests Veillonella.",
87
+ "Aerobic growth is inconsistent with A. fermentans.",
88
+ "Rod-shaped morphology excludes this species."
89
+ ],
90
+
91
+ "recommended_next_tests": [
92
+ {
93
+ "test": "Anaerobic growth verification",
94
+ "reason": "Confirms obligate anaerobic metabolism."
95
+ },
96
+ {
97
+ "test": "MALDI-TOF MS",
98
+ "reason": "Reliable identification due to limited biochemical activity."
99
+ }
100
+ ]
101
+ }
data/rag/knowledge_base/Acidaminococcus/genus.json ADDED
@@ -0,0 +1,131 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Acidaminococcus",
5
+
6
+ "overview": {
7
+ "short": "Acidaminococcus species are Gram-negative, anaerobic cocci belonging to the class Negativicutes, characterized by amino acid fermentation rather than carbohydrate metabolism.",
8
+ "clinical_context": "Part of the normal gastrointestinal flora and occasionally isolated from polymicrobial anaerobic infections."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Negative",
13
+ "Shape": "Cocci",
14
+ "Motility": "Negative",
15
+ "Capsule": "Unknown",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Negative",
18
+ "Haemolysis Type": "None",
19
+ "Media Grown On": [
20
+ "Blood Agar"
21
+ ],
22
+ "Colony Morphology": [
23
+ "Small",
24
+ "Grey",
25
+ "Convex"
26
+ ],
27
+ "Oxygen Requirement": "Obligate Anaerobe",
28
+ "Growth Temperature": "35//37",
29
+ "Catalase": "Negative",
30
+ "Oxidase": "Negative",
31
+ "Indole": "Negative",
32
+ "Urease": "Negative",
33
+ "Citrate": "Negative",
34
+ "Methyl Red": "Negative",
35
+ "VP": "Negative",
36
+ "H2S": "Negative",
37
+ "DNase": "Negative",
38
+ "ONPG": "Negative",
39
+ "Coagulase": "Negative",
40
+ "Gelatin Hydrolysis": "Negative",
41
+ "Esculin Hydrolysis": "Negative",
42
+ "Nitrate Reduction": "Negative",
43
+ "NaCl Tolerant (>=6%)": "Negative",
44
+ "Lipase Test": "Negative",
45
+ "Lysine Decarboxylase": "Negative",
46
+ "Ornithine Decarboxylase": "Negative",
47
+ "Ornitihine Decarboxylase": "Negative",
48
+ "Arginine dihydrolase": "Negative",
49
+ "Glucose Fermentation": "Negative",
50
+ "Lactose Fermentation": "Negative",
51
+ "Sucrose Fermentation": "Negative",
52
+ "Maltose Fermentation": "Negative",
53
+ "Mannitol Fermentation": "Negative",
54
+ "Sorbitol Fermentation": "Negative",
55
+ "Xylose Fermentation": "Negative",
56
+ "Rhamnose Fermentation": "Negative",
57
+ "Arabinose Fermentation": "Negative",
58
+ "Raffinose Fermentation": "Negative",
59
+ "Trehalose Fermentation": "Negative",
60
+ "Inositol Fermentation": "Negative",
61
+ "Gas Production": "Negative",
62
+ "TSI Pattern": "K/K",
63
+ "Colony Pattern": "Unknown",
64
+ "Pigment": "None",
65
+ "Motility Type": "None"
66
+ },
67
+
68
+ "field_notes": {
69
+ "Gram Stain": "Despite being Gram-negative, Acidaminococcus belongs to a lineage phylogenetically related to Gram-positive bacteria.",
70
+ "Glucose Fermentation": "Species do not ferment carbohydrates and instead utilize amino acids for energy.",
71
+ "Oxygen Requirement": "Strict anaerobiosis is a defining characteristic."
72
+ },
73
+
74
+ "key_differentiators": [
75
+ {
76
+ "field": "Oxygen Requirement",
77
+ "expected": "Obligate Anaerobe",
78
+ "distinguishes_from": ["Neisseria", "Veillonella"],
79
+ "notes": "Strict anaerobic growth separates Acidaminococcus from aerobic Gram-negative cocci."
80
+ },
81
+ {
82
+ "field": "Shape",
83
+ "expected": "Cocci",
84
+ "distinguishes_from": ["Bacteroides", "Fusobacterium"],
85
+ "notes": "Coccoid morphology helps differentiate from anaerobic Gram-negative rods."
86
+ },
87
+ {
88
+ "field": "Glucose Fermentation",
89
+ "expected": "Negative",
90
+ "distinguishes_from": ["Veillonella"],
91
+ "notes": "Lack of carbohydrate fermentation supports Acidaminococcus."
92
+ }
93
+ ],
94
+
95
+ "common_confusions": [
96
+ {
97
+ "genus": "Veillonella",
98
+ "reason": "Both are anaerobic Gram-negative cocci isolated from similar clinical contexts."
99
+ },
100
+ {
101
+ "genus": "Megasphaera",
102
+ "reason": "Phylogenetic relatedness within Negativicutes."
103
+ }
104
+ ],
105
+
106
+ "when_to_question_identification": [
107
+ "Aerobic or facultative growth argues against Acidaminococcus.",
108
+ "Carbohydrate fermentation suggests Veillonella.",
109
+ "Rod-shaped morphology excludes this genus."
110
+ ],
111
+
112
+ "recommended_next_tests": [
113
+ {
114
+ "test": "Anaerobic growth confirmation",
115
+ "reason": "Essential for correct genus assignment."
116
+ },
117
+ {
118
+ "test": "Amino acid fermentation profiling",
119
+ "reason": "Characteristic metabolic feature of Acidaminococcus."
120
+ },
121
+ {
122
+ "test": "MALDI-TOF MS",
123
+ "reason": "Recommended due to biochemical inertness and rarity."
124
+ }
125
+ ],
126
+
127
+ "supported_species": [
128
+ "fermentans",
129
+ "intestini"
130
+ ]
131
+ }
data/rag/knowledge_base/Acidaminococcus/intestini.json ADDED
@@ -0,0 +1,101 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acidaminococcus",
5
+ "species": "intestini",
6
+
7
+ "overview": {
8
+ "short": "Acidaminococcus intestini is a Gram-negative, obligately anaerobic coccus primarily associated with the human intestinal microbiota.",
9
+ "clinical_context": "Rarely isolated in clinical specimens and most often identified during microbiome or research studies."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Cocci",
15
+ "Motility": "Negative",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Small",
25
+ "Grey",
26
+ "Convex"
27
+ ],
28
+ "Oxygen Requirement": "Obligate Anaerobe",
29
+ "Growth Temperature": "35//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Negative",
33
+ "Urease": "Negative",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Negative",
36
+ "VP": "Negative",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Negative",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Negative",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Negative",
47
+ "Ornithine Decarboxylase": "Negative",
48
+ "Ornitihine Decarboxylase": "Negative",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Negative",
51
+ "Lactose Fermentation": "Negative",
52
+ "Sucrose Fermentation": "Negative",
53
+ "Maltose Fermentation": "Negative",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Negative",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Negative",
60
+ "Trehalose Fermentation": "Negative",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "K/K",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Clinical Isolation Frequency",
72
+ "value": "Rare",
73
+ "importance": "medium",
74
+ "notes": "Less frequently encountered in diagnostic microbiology compared to A. fermentans."
75
+ }
76
+ ],
77
+
78
+ "common_confusions": [
79
+ {
80
+ "genus": "Veillonella",
81
+ "reason": "Similar anaerobic Gram-negative cocci morphology."
82
+ }
83
+ ],
84
+
85
+ "when_to_question_identification": [
86
+ "Isolation from normally sterile sites is unusual.",
87
+ "Carbohydrate fermentation suggests misidentification.",
88
+ "Growth in aerobic conditions excludes this species."
89
+ ],
90
+
91
+ "recommended_next_tests": [
92
+ {
93
+ "test": "MALDI-TOF MS",
94
+ "reason": "Primary method for distinguishing rare anaerobic cocci."
95
+ },
96
+ {
97
+ "test": "16S rRNA sequencing",
98
+ "reason": "Recommended for confirmation due to rarity."
99
+ }
100
+ ]
101
+ }
data/rag/knowledge_base/Acidovorax/avenae.json ADDED
@@ -0,0 +1,107 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acidovorax",
5
+ "species": "avenae",
6
+
7
+ "overview": {
8
+ "short": "Acidovorax avenae is an aerobic, oxidase-positive, non-fermentative Gram-negative rod primarily associated with plants.",
9
+ "clinical_context": "Rarely isolated from human specimens; most recoveries represent environmental or contaminant organisms."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Nutrient Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Non-pigmented"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "20//30",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Variable",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Growth Temperature",
73
+ "value": "20//30",
74
+ "importance": "high",
75
+ "notes": "Lower optimal growth temperature supports environmental origin."
76
+ },
77
+ {
78
+ "field": "Nitrate Reduction",
79
+ "value": "Negative",
80
+ "importance": "medium",
81
+ "notes": "Helps separate from denitrifying Acidovorax species."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Acidovorax citrulli",
88
+ "reason": "Shared non-fermentative and oxidase-positive profile."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Growth at 37°C suggests another species.",
94
+ "Clinical significance without environmental context is unusual."
95
+ ],
96
+
97
+ "recommended_next_tests": [
98
+ {
99
+ "test": "Growth temperature assessment",
100
+ "reason": "Helps distinguish environmental Acidovorax species."
101
+ },
102
+ {
103
+ "test": "MALDI-TOF MS",
104
+ "reason": "Reliable species-level identification."
105
+ }
106
+ ]
107
+ }
data/rag/knowledge_base/Acidovorax/citrulli.json ADDED
@@ -0,0 +1,101 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acidovorax",
5
+ "species": "citrulli",
6
+
7
+ "overview": {
8
+ "short": "Acidovorax citrulli is an aerobic, oxidase-positive, non-fermentative Gram-negative rod best known as a plant pathogen.",
9
+ "clinical_context": "Human isolation is rare and typically reflects environmental exposure rather than infection."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Nutrient Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Non-pigmented"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "25//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Variable",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Growth Temperature",
73
+ "value": "25//37",
74
+ "importance": "medium",
75
+ "notes": "Broader growth range compared to A. avenae."
76
+ }
77
+ ],
78
+
79
+ "common_confusions": [
80
+ {
81
+ "species": "Acidovorax avenae",
82
+ "reason": "Overlapping biochemical reactions."
83
+ }
84
+ ],
85
+
86
+ "when_to_question_identification": [
87
+ "Isolation from sterile clinical sites without exposure history.",
88
+ "Anaerobic growth is incompatible."
89
+ ],
90
+
91
+ "recommended_next_tests": [
92
+ {
93
+ "test": "Growth temperature profiling",
94
+ "reason": "Supports species-level distinction."
95
+ },
96
+ {
97
+ "test": "MALDI-TOF MS",
98
+ "reason": "Preferred identification method."
99
+ }
100
+ ]
101
+ }
data/rag/knowledge_base/Acidovorax/delafieldii.json ADDED
@@ -0,0 +1,111 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acidovorax",
5
+ "species": "delafieldii",
6
+
7
+ "overview": {
8
+ "short": "Acidovorax delafieldii is an aerobic, oxidase-positive, non-fermentative Gram-negative rod commonly recovered from soil and water.",
9
+ "clinical_context": "Occasional opportunistic isolation in immunocompromised patients."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Unknown",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Nutrient Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Non-pigmented"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "20//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Positive",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Positive",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Citrate",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Distinguishes A. delafieldii from other Acidovorax species."
76
+ },
77
+ {
78
+ "field": "Nitrate Reduction",
79
+ "value": "Positive",
80
+ "importance": "medium",
81
+ "notes": "Supports identification when combined with citrate positivity."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Acidovorax avenae",
88
+ "reason": "Shared environmental origin and biochemical overlap."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Oxidase negativity suggests alternative genera.",
94
+ "Fermentative metabolism excludes Acidovorax."
95
+ ],
96
+
97
+ "recommended_next_tests": [
98
+ {
99
+ "test": "Citrate utilization",
100
+ "reason": "Key species discriminator."
101
+ },
102
+ {
103
+ "test": "Nitrate reduction",
104
+ "reason": "Supports identification."
105
+ },
106
+ {
107
+ "test": "MALDI-TOF MS",
108
+ "reason": "Preferred confirmatory method."
109
+ }
110
+ ]
111
+ }
data/rag/knowledge_base/Acidovorax/genus.json ADDED
@@ -0,0 +1,133 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Acidovorax",
5
+
6
+ "overview": {
7
+ "short": "Acidovorax species are Gram-negative, aerobic, non-fermentative rods belonging to the family Comamonadaceae.",
8
+ "clinical_context": "Primarily environmental organisms, occasionally isolated from respiratory specimens or opportunistic infections, especially in immunocompromised patients."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Negative",
13
+ "Shape": "Rods",
14
+ "Motility": "Positive",
15
+ "Capsule": "Unknown",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Negative",
18
+ "Haemolysis Type": "None",
19
+ "Media Grown On": [
20
+ "Blood Agar",
21
+ "Nutrient Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Smooth",
25
+ "Grey",
26
+ "Non-pigmented"
27
+ ],
28
+ "Oxygen Requirement": "Aerobic",
29
+ "Growth Temperature": "20//37",
30
+ "Catalase": "Positive",
31
+ "Oxidase": "Positive",
32
+ "Indole": "Negative",
33
+ "Urease": "Negative",
34
+ "Citrate": "Variable",
35
+ "Methyl Red": "Negative",
36
+ "VP": "Negative",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Negative",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Variable",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Variable",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Negative",
47
+ "Ornithine Decarboxylase": "Negative",
48
+ "Ornitihine Decarboxylase": "Negative",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Negative",
51
+ "Lactose Fermentation": "Negative",
52
+ "Sucrose Fermentation": "Negative",
53
+ "Maltose Fermentation": "Negative",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Negative",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Negative",
60
+ "Trehalose Fermentation": "Negative",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "K/K",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "Polar"
67
+ },
68
+
69
+ "field_notes": {
70
+ "Glucose Fermentation": "Acidovorax species are non-fermentative and rely on oxidative metabolism.",
71
+ "Oxidase": "Oxidase positivity is a key feature separating Acidovorax from many Enterobacterales.",
72
+ "Motility": "Typically motile with polar flagella."
73
+ },
74
+
75
+ "key_differentiators": [
76
+ {
77
+ "field": "Oxidase",
78
+ "expected": "Positive",
79
+ "distinguishes_from": ["Enterobacter", "Escherichia"],
80
+ "notes": "Oxidase positivity supports non-fermentative genera."
81
+ },
82
+ {
83
+ "field": "Glucose Fermentation",
84
+ "expected": "Negative",
85
+ "distinguishes_from": ["Enterobacter", "Klebsiella"],
86
+ "notes": "Non-fermentative metabolism differentiates from Enterobacterales."
87
+ },
88
+ {
89
+ "field": "Oxygen Requirement",
90
+ "expected": "Aerobic",
91
+ "distinguishes_from": ["Acidaminococcus"],
92
+ "notes": "Strict aerobic growth separates from anaerobic Gram-negative cocci."
93
+ }
94
+ ],
95
+
96
+ "common_confusions": [
97
+ {
98
+ "genus": "Comamonas",
99
+ "reason": "Shared family membership and overlapping biochemical profiles."
100
+ },
101
+ {
102
+ "genus": "Burkholderia",
103
+ "reason": "Both are oxidase-positive, non-fermentative Gram-negative rods."
104
+ }
105
+ ],
106
+
107
+ "when_to_question_identification": [
108
+ "Glucose fermentation suggests Enterobacterales.",
109
+ "Oxidase negativity argues against Acidovorax.",
110
+ "Anaerobic growth is incompatible with this genus."
111
+ ],
112
+
113
+ "recommended_next_tests": [
114
+ {
115
+ "test": "Oxidase test",
116
+ "reason": "Confirms placement among non-fermentative Gram-negative rods."
117
+ },
118
+ {
119
+ "test": "MALDI-TOF MS",
120
+ "reason": "Reliable genus-level identification within Comamonadaceae."
121
+ },
122
+ {
123
+ "test": "Molecular identification",
124
+ "reason": "Recommended for species-level resolution due to biochemical overlap."
125
+ }
126
+ ],
127
+
128
+ "supported_species": [
129
+ "temperans",
130
+ "avenae",
131
+ "citrulli"
132
+ ]
133
+ }
data/rag/knowledge_base/Acinetobacter/baumannii.json ADDED
@@ -0,0 +1,115 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acinetobacter",
5
+ "species": "baumannii",
6
+
7
+ "overview": {
8
+ "short": "Acinetobacter baumannii is a Gram-negative, strictly aerobic, non-fermentative coccobacillus associated with severe healthcare-associated infections.",
9
+ "clinical_context": "A major cause of ventilator-associated pneumonia, bloodstream infections, wound infections, and outbreaks in intensive care units."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Coccobacilli",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Opaque",
27
+ "Grey-White"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "20//44",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Variable",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Variable",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Variable",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Positive",
46
+ "Lipase Test": "Variable",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "NaCl Tolerant (>=6%)",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Salt tolerance supports A. baumannii over many other Acinetobacter species."
76
+ },
77
+ {
78
+ "field": "Growth Temperature",
79
+ "value": "44//44",
80
+ "importance": "high",
81
+ "notes": "Growth at elevated temperatures is characteristic of A. baumannii."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Acinetobacter pittii",
88
+ "reason": "Part of the A. baumannii complex with overlapping biochemical profiles."
89
+ },
90
+ {
91
+ "species": "Acinetobacter calcoaceticus",
92
+ "reason": "Closely related environmental species within the complex."
93
+ }
94
+ ],
95
+
96
+ "when_to_question_identification": [
97
+ "Failure to grow at elevated temperatures suggests a non-baumannii species.",
98
+ "Environmental isolation without clinical context may indicate another Acinetobacter species."
99
+ ],
100
+
101
+ "recommended_next_tests": [
102
+ {
103
+ "test": "MALDI-TOF MS",
104
+ "reason": "Accurate differentiation within the Acinetobacter baumannii complex."
105
+ },
106
+ {
107
+ "test": "Antimicrobial susceptibility testing",
108
+ "reason": "Critical due to frequent multidrug resistance."
109
+ },
110
+ {
111
+ "test": "Molecular identification",
112
+ "reason": "Definitive species-level confirmation when clinically significant."
113
+ }
114
+ ]
115
+ }
data/rag/knowledge_base/Acinetobacter/calcoaceticus.json ADDED
@@ -0,0 +1,103 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acinetobacter",
5
+ "species": "calcoaceticus",
6
+
7
+ "overview": {
8
+ "short": "Acinetobacter calcoaceticus is a Gram-negative, aerobic, non-fermentative coccobacillus primarily associated with environmental sources.",
9
+ "clinical_context": "Rarely implicated in human disease and most often recovered from soil, water, and hospital environments."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Coccobacilli",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Dry"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "15//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Growth Temperature",
73
+ "value": "37//37",
74
+ "importance": "high",
75
+ "notes": "Inability to grow at higher temperatures helps exclude pathogenic Acinetobacter species."
76
+ },
77
+ {
78
+ "field": "NaCl Tolerant (>=6%)",
79
+ "value": "Negative",
80
+ "importance": "high",
81
+ "notes": "Lack of salt tolerance differentiates A. calcoaceticus from A. baumannii."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Acinetobacter pittii",
88
+ "reason": "Closely related within the A. baumannii complex, but more clinically relevant."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Isolation from severe clinical infections suggests another Acinetobacter species.",
94
+ "Growth at elevated temperatures argues against A. calcoaceticus."
95
+ ],
96
+
97
+ "recommended_next_tests": [
98
+ {
99
+ "test": "MALDI-TOF MS",
100
+ "reason": "Required to distinguish environmental Acinetobacter species."
101
+ }
102
+ ]
103
+ }
data/rag/knowledge_base/Acinetobacter/genus.json ADDED
@@ -0,0 +1,135 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Acinetobacter",
5
+
6
+ "overview": {
7
+ "short": "Acinetobacter species are Gram-negative, strictly aerobic, non-fermentative coccobacilli widely distributed in the environment.",
8
+ "clinical_context": "Clinically significant species, particularly Acinetobacter baumannii, are important causes of healthcare-associated infections."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Negative",
13
+ "Shape": "Coccobacilli",
14
+ "Motility": "Negative",
15
+ "Capsule": "Variable",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Negative",
18
+ "Haemolysis Type": "None",
19
+ "Media Grown On": [
20
+ "Blood Agar",
21
+ "MacConkey Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Smooth",
25
+ "Opaque",
26
+ "Grey-White"
27
+ ],
28
+ "Oxygen Requirement": "Aerobic",
29
+ "Growth Temperature": "20//44",
30
+ "Catalase": "Positive",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Negative",
33
+ "Urease": "Variable",
34
+ "Citrate": "Variable",
35
+ "Methyl Red": "Negative",
36
+ "VP": "Negative",
37
+ "H2S": "Negative",
38
+ "DNase": "Variable",
39
+ "ONPG": "Negative",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Variable",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Negative",
44
+ "NaCl Tolerant (>=6%)": "Variable",
45
+ "Lipase Test": "Variable",
46
+ "Lysine Decarboxylase": "Negative",
47
+ "Ornithine Decarboxylase": "Negative",
48
+ "Ornitihine Decarboxylase": "Negative",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Negative",
51
+ "Lactose Fermentation": "Negative",
52
+ "Sucrose Fermentation": "Negative",
53
+ "Maltose Fermentation": "Negative",
54
+ "Mannitol Fermentation": "Variable",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Negative",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Negative",
60
+ "Trehalose Fermentation": "Negative",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "K/K",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "field_notes": {
70
+ "Motility": "Acinetobacter species are characteristically non-motile.",
71
+ "Oxidase": "Oxidase negativity is a key differentiator from many other non-fermenters.",
72
+ "Shape": "Often appear as plump coccobacilli on Gram stain."
73
+ },
74
+
75
+ "key_differentiators": [
76
+ {
77
+ "field": "Oxidase",
78
+ "expected": "Negative",
79
+ "distinguishes_from": ["Pseudomonas", "Burkholderia"],
80
+ "notes": "Oxidase negativity is critical in separating Acinetobacter from most non-fermenters."
81
+ },
82
+ {
83
+ "field": "Motility",
84
+ "expected": "Negative",
85
+ "distinguishes_from": ["Stenotrophomonas", "Alcaligenes"],
86
+ "notes": "Non-motility supports Acinetobacter."
87
+ },
88
+ {
89
+ "field": "Glucose Fermentation",
90
+ "expected": "Negative",
91
+ "distinguishes_from": ["Enterobacterales"],
92
+ "notes": "Non-fermentative metabolism excludes Enterobacterales."
93
+ }
94
+ ],
95
+
96
+ "common_confusions": [
97
+ {
98
+ "genus": "Pseudomonas",
99
+ "reason": "Shared non-fermentative metabolism but differs by oxidase status."
100
+ },
101
+ {
102
+ "genus": "Stenotrophomonas",
103
+ "reason": "Overlapping non-fermentative profile with variable biochemical reactions."
104
+ }
105
+ ],
106
+
107
+ "when_to_question_identification": [
108
+ "Oxidase positivity argues against Acinetobacter.",
109
+ "Motility suggests an alternative non-fermenter.",
110
+ "Anaerobic growth is inconsistent."
111
+ ],
112
+
113
+ "recommended_next_tests": [
114
+ {
115
+ "test": "Oxidase test",
116
+ "reason": "Primary discriminator among non-fermenters."
117
+ },
118
+ {
119
+ "test": "MALDI-TOF MS",
120
+ "reason": "Reliable genus- and species-level identification."
121
+ },
122
+ {
123
+ "test": "Antimicrobial susceptibility testing",
124
+ "reason": "Clinically important due to frequent multidrug resistance."
125
+ }
126
+ ],
127
+
128
+ "supported_species": [
129
+ "baumannii",
130
+ "calcoaceticus",
131
+ "lwoffii",
132
+ "johnsonii",
133
+ "pittii"
134
+ ]
135
+ }
data/rag/knowledge_base/Acinetobacter/johnsonii.json ADDED
@@ -0,0 +1,97 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acinetobacter",
5
+ "species": "johnsonii",
6
+
7
+ "overview": {
8
+ "short": "Acinetobacter johnsonii is a Gram-negative, aerobic, non-fermentative coccobacillus commonly recovered from environmental sources.",
9
+ "clinical_context": "Rarely associated with human infection and typically considered of low pathogenic potential."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Coccobacilli",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Dry"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "15//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Growth Temperature",
73
+ "value": "37//37",
74
+ "importance": "medium",
75
+ "notes": "Does not tolerate higher temperatures typical of A. baumannii."
76
+ }
77
+ ],
78
+
79
+ "common_confusions": [
80
+ {
81
+ "species": "Acinetobacter lwoffii",
82
+ "reason": "Similar low biochemical activity and environmental presence."
83
+ }
84
+ ],
85
+
86
+ "when_to_question_identification": [
87
+ "Isolation from severe clinical infections may indicate another species.",
88
+ "Growth at elevated temperatures argues against A. johnsonii."
89
+ ],
90
+
91
+ "recommended_next_tests": [
92
+ {
93
+ "test": "MALDI-TOF MS",
94
+ "reason": "Definitive species-level identification."
95
+ }
96
+ ]
97
+ }
data/rag/knowledge_base/Acinetobacter/lwoffii.json ADDED
@@ -0,0 +1,103 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acinetobacter",
5
+ "species": "lwoffii",
6
+
7
+ "overview": {
8
+ "short": "Acinetobacter lwoffii is a Gram-negative, aerobic, non-fermentative coccobacillus commonly found as part of normal skin flora.",
9
+ "clinical_context": "Occasionally associated with opportunistic infections, particularly in immunocompromised patients."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Coccobacilli",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Grey",
27
+ "Dry"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "20//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "NaCl Tolerant (>=6%)",
73
+ "value": "Negative",
74
+ "importance": "high",
75
+ "notes": "Lack of salt tolerance helps distinguish A. lwoffii from A. baumannii."
76
+ },
77
+ {
78
+ "field": "Growth Temperature",
79
+ "value": "37//37",
80
+ "importance": "medium",
81
+ "notes": "Limited growth at higher temperatures compared to A. baumannii."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Acinetobacter johnsonii",
88
+ "reason": "Similar biochemical inactivity and environmental distribution."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Growth at high temperatures suggests A. baumannii.",
94
+ "Isolation from sterile sites may warrant further confirmation."
95
+ ],
96
+
97
+ "recommended_next_tests": [
98
+ {
99
+ "test": "MALDI-TOF MS",
100
+ "reason": "Reliable discrimination among Acinetobacter species."
101
+ }
102
+ ]
103
+ }
data/rag/knowledge_base/Acinetobacter/pittii.json ADDED
@@ -0,0 +1,111 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Acinetobacter",
5
+ "species": "pittii",
6
+
7
+ "overview": {
8
+ "short": "Acinetobacter pittii is a Gram-negative, aerobic, non-fermentative coccobacillus belonging to the Acinetobacter baumannii complex.",
9
+ "clinical_context": "Associated with opportunistic infections including bloodstream, respiratory, and wound infections, generally less virulent than A. baumannii."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Coccobacilli",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Smooth",
26
+ "Opaque",
27
+ "Grey-White"
28
+ ],
29
+ "Oxygen Requirement": "Aerobic",
30
+ "Growth Temperature": "20//40",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Variable",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Variable",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Variable",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Variable",
46
+ "Lipase Test": "Variable",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Negative",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "K/K",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Growth Temperature",
73
+ "value": "40//40",
74
+ "importance": "high",
75
+ "notes": "Typically does not grow at the higher temperatures tolerated by A. baumannii."
76
+ },
77
+ {
78
+ "field": "NaCl Tolerant (>=6%)",
79
+ "value": "Variable",
80
+ "importance": "medium",
81
+ "notes": "Reduced salt tolerance compared to A. baumannii."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Acinetobacter baumannii",
88
+ "reason": "Part of the A. baumannii complex with overlapping biochemical characteristics."
89
+ },
90
+ {
91
+ "species": "Acinetobacter calcoaceticus",
92
+ "reason": "Genetically related environmental species within the complex."
93
+ }
94
+ ],
95
+
96
+ "when_to_question_identification": [
97
+ "Growth at ≥44°C suggests A. baumannii.",
98
+ "Strong salt tolerance supports A. baumannii over A. pittii."
99
+ ],
100
+
101
+ "recommended_next_tests": [
102
+ {
103
+ "test": "MALDI-TOF MS",
104
+ "reason": "Primary method for differentiating species within the A. baumannii complex."
105
+ },
106
+ {
107
+ "test": "Molecular identification",
108
+ "reason": "Definitive resolution when clinical significance is high."
109
+ }
110
+ ]
111
+ }
data/rag/knowledge_base/Actinobacillus/actinomycetemcomitans.json ADDED
@@ -0,0 +1,112 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Actinobacillus",
5
+ "species": "actinomycetemcomitans",
6
+
7
+ "overview": {
8
+ "short": "Actinobacillus actinomycetemcomitans is a Gram-negative coccobacillus associated with periodontal disease.",
9
+ "clinical_context": "Commonly isolated from oral infections, endocarditis, and periodontal lesions in humans."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Short Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Chocolate Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Small",
26
+ "Grey",
27
+ "Smooth",
28
+ "Star-shaped internal structure"
29
+ ],
30
+ "Oxygen Requirement": "Facultative Anaerobe",
31
+ "Growth Temperature": "35//37",
32
+ "Catalase": "Positive",
33
+ "Oxidase": "Negative",
34
+ "Indole": "Negative",
35
+ "Urease": "Negative",
36
+ "Citrate": "Negative",
37
+ "Methyl Red": "Negative",
38
+ "VP": "Negative",
39
+ "H2S": "Negative",
40
+ "DNase": "Negative",
41
+ "ONPG": "Negative",
42
+ "Coagulase": "Negative",
43
+ "Gelatin Hydrolysis": "Negative",
44
+ "Esculin Hydrolysis": "Negative",
45
+ "Nitrate Reduction": "Variable",
46
+ "NaCl Tolerant (>=6%)": "Negative",
47
+ "Lipase Test": "Negative",
48
+ "Lysine Decarboxylase": "Negative",
49
+ "Ornithine Decarboxylase": "Negative",
50
+ "Ornitihine Decarboxylase": "Negative",
51
+ "Arginine dihydrolase": "Negative",
52
+ "Glucose Fermentation": "Positive",
53
+ "Lactose Fermentation": "Negative",
54
+ "Sucrose Fermentation": "Variable",
55
+ "Maltose Fermentation": "Variable",
56
+ "Mannitol Fermentation": "Variable",
57
+ "Sorbitol Fermentation": "Negative",
58
+ "Xylose Fermentation": "Variable",
59
+ "Rhamnose Fermentation": "Negative",
60
+ "Arabinose Fermentation": "Variable",
61
+ "Raffinose Fermentation": "Negative",
62
+ "Trehalose Fermentation": "Variable",
63
+ "Inositol Fermentation": "Negative",
64
+ "Gas Production": "Negative",
65
+ "TSI Pattern": "A/A",
66
+ "Colony Pattern": "Unknown",
67
+ "Pigment": "None",
68
+ "Motility Type": "None"
69
+ },
70
+
71
+ "species_markers": [
72
+ {
73
+ "field": "Colony Morphology",
74
+ "value": "Star-shaped internal structure",
75
+ "importance": "high",
76
+ "notes": "Characteristic colony appearance aids identification."
77
+ },
78
+ {
79
+ "field": "Clinical context",
80
+ "value": "Periodontal disease",
81
+ "importance": "high",
82
+ "notes": "Strong association with oral infections."
83
+ }
84
+ ],
85
+
86
+ "common_confusions": [
87
+ {
88
+ "genus": "Haemophilus",
89
+ "reason": "Similar growth requirements and oral habitat."
90
+ },
91
+ {
92
+ "genus": "Aggregatibacter",
93
+ "reason": "Taxonomic overlap and similar biochemical profiles."
94
+ }
95
+ ],
96
+
97
+ "when_to_question_identification": [
98
+ "Strong haemolysis suggests veterinary Actinobacillus species.",
99
+ "Lack of star-shaped colony morphology requires confirmation."
100
+ ],
101
+
102
+ "recommended_next_tests": [
103
+ {
104
+ "test": "MALDI-TOF MS",
105
+ "reason": "Reliable species-level identification."
106
+ },
107
+ {
108
+ "test": "16S rRNA sequencing",
109
+ "reason": "Used when phenotypic identification is inconclusive."
110
+ }
111
+ ]
112
+ }
data/rag/knowledge_base/Actinobacillus/genus.json ADDED
@@ -0,0 +1,134 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Actinobacillus",
5
+
6
+ "overview": {
7
+ "short": "Actinobacillus species are small, Gram-negative, facultatively anaerobic coccobacilli belonging to the Pasteurellaceae family, commonly associated with mucosal surfaces.",
8
+ "clinical_context": "Primarily associated with respiratory tract infections, oral infections, and invasive disease in both humans and animals."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Negative",
13
+ "Shape": "Short Rods",
14
+ "Motility": "Negative",
15
+ "Capsule": "Variable",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Variable",
18
+ "Haemolysis Type": "Variable",
19
+ "Media Grown On": [
20
+ "Blood Agar",
21
+ "Chocolate Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Small",
25
+ "Grey",
26
+ "Smooth",
27
+ "Non-pigmented"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "35//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Variable",
33
+ "Indole": "Variable",
34
+ "Urease": "Variable",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Variable",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Variable",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Variable",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Variable",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "A/A",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "field_notes": {
71
+ "Shape": "Often described as coccobacilli or short rods; may appear pleomorphic.",
72
+ "Growth Requirements": "Many species require enriched media and may grow poorly on MacConkey Agar.",
73
+ "Oxidase": "Reaction varies by species and is not genus-defining."
74
+ },
75
+
76
+ "key_differentiators": [
77
+ {
78
+ "field": "Growth on MacConkey Agar",
79
+ "expected": "Negative",
80
+ "distinguishes_from": ["Enterobacter", "Escherichia"],
81
+ "notes": "Poor or absent growth on MacConkey Agar helps separate Actinobacillus from Enterobacterales."
82
+ },
83
+ {
84
+ "field": "Motility",
85
+ "expected": "Negative",
86
+ "distinguishes_from": ["Achromobacter", "Pseudomonas"],
87
+ "notes": "Non-motility helps differentiate from motile non-fermenters."
88
+ },
89
+ {
90
+ "field": "ONPG",
91
+ "expected": "Negative",
92
+ "distinguishes_from": ["Haemophilus"],
93
+ "notes": "Helps separate Actinobacillus from some closely related Pasteurellaceae."
94
+ }
95
+ ],
96
+
97
+ "common_confusions": [
98
+ {
99
+ "genus": "Haemophilus",
100
+ "reason": "Shared family Pasteurellaceae, similar morphology, and overlapping growth requirements."
101
+ },
102
+ {
103
+ "genus": "Aggregatibacter",
104
+ "reason": "Similar clinical niche and biochemical overlap, particularly in oral infections."
105
+ }
106
+ ],
107
+
108
+ "when_to_question_identification": [
109
+ "Strong oxidase positivity and motility suggest Achromobacter or other non-fermenters.",
110
+ "Robust growth on MacConkey Agar argues against Actinobacillus.",
111
+ "Indole-positive isolates require careful species-level confirmation."
112
+ ],
113
+
114
+ "recommended_next_tests": [
115
+ {
116
+ "test": "Growth factor requirement testing (X and V factors)",
117
+ "reason": "Helps differentiate Actinobacillus from Haemophilus species."
118
+ },
119
+ {
120
+ "test": "Oxidase and indole testing",
121
+ "reason": "Useful for species-level discrimination within Pasteurellaceae."
122
+ },
123
+ {
124
+ "test": "MALDI-TOF MS",
125
+ "reason": "Reliable genus and species-level identification due to phenotypic overlap."
126
+ }
127
+ ],
128
+
129
+ "supported_species": [
130
+ "actinomycetemcomitans",
131
+ "lignieresii",
132
+ "ureae"
133
+ ]
134
+ }
data/rag/knowledge_base/Actinobacillus/pleuropneumoniae.json ADDED
@@ -0,0 +1,103 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Actinobacillus",
5
+ "species": "pleuropneumoniae",
6
+
7
+ "overview": {
8
+ "short": "Actinobacillus pleuropneumoniae is a Gram-negative coccobacillus causing severe respiratory disease in swine.",
9
+ "clinical_context": "A major cause of porcine pleuropneumonia; not considered a human pathogen."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Short Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Positive",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Positive",
19
+ "Haemolysis Type": "Beta",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Chocolate Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Small",
26
+ "Grey",
27
+ "Smooth"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "35//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Variable",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Variable",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Variable",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "A/A",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Oxidase",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Helps distinguish from other Actinobacillus species."
76
+ },
77
+ {
78
+ "field": "Host specificity",
79
+ "value": "Swine",
80
+ "importance": "high",
81
+ "notes": "Strongly associated with porcine hosts."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Actinobacillus suis",
88
+ "reason": "Shared haemolysis and overlapping veterinary context."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Isolation from human samples suggests misidentification.",
94
+ "Non-haemolytic isolates are inconsistent with A. pleuropneumoniae."
95
+ ],
96
+
97
+ "recommended_next_tests": [
98
+ {
99
+ "test": "Veterinary PCR panels",
100
+ "reason": "Gold standard for definitive identification."
101
+ }
102
+ ]
103
+ }
data/rag/knowledge_base/Actinobacillus/suis.json ADDED
@@ -0,0 +1,103 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Actinobacillus",
5
+ "species": "suis",
6
+
7
+ "overview": {
8
+ "short": "Actinobacillus suis is a Gram-negative coccobacillus primarily associated with invasive infections in swine.",
9
+ "clinical_context": "Rare in humans; primarily a veterinary pathogen causing septicemia, pneumonia, and meningitis in pigs."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Short Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Positive",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Positive",
19
+ "Haemolysis Type": "Beta",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Chocolate Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Small",
26
+ "Grey",
27
+ "Smooth"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "35//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Variable",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Variable",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Variable",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Variable",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "A/A",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Haemolysis",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Beta-haemolysis supports differentiation from non-haemolytic Actinobacillus species."
76
+ },
77
+ {
78
+ "field": "Capsule",
79
+ "value": "Positive",
80
+ "importance": "medium",
81
+ "notes": "Capsule contributes to virulence in animal infections."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Actinobacillus pleuropneumoniae",
88
+ "reason": "Both are haemolytic and primarily veterinary pathogens."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Human clinical isolation should prompt re-evaluation.",
94
+ "Non-haemolytic isolates are inconsistent with A. suis."
95
+ ],
96
+
97
+ "recommended_next_tests": [
98
+ {
99
+ "test": "Veterinary MALDI-TOF reference",
100
+ "reason": "Required for accurate differentiation from related animal pathogens."
101
+ }
102
+ ]
103
+ }
data/rag/knowledge_base/Actinomyces/genus.json ADDED
@@ -0,0 +1,135 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Actinomyces",
5
+
6
+ "overview": {
7
+ "short": "Actinomyces species are Gram-positive, non-spore-forming, pleomorphic rods that commonly inhabit the human oral cavity, gastrointestinal tract, and female genital tract.",
8
+ "clinical_context": "Associated with chronic, suppurative infections (actinomycosis), often involving abscess formation and sinus tracts, typically in cervicofacial, thoracic, or abdominopelvic sites."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Positive",
13
+ "Shape": "Rods",
14
+ "Motility": "Negative",
15
+ "Capsule": "Negative",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Negative",
18
+ "Haemolysis Type": "None",
19
+ "Media Grown On": [
20
+ "Blood Agar"
21
+ ],
22
+ "Colony Morphology": [
23
+ "White",
24
+ "Grey",
25
+ "Rough",
26
+ "Irregular"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "30//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Variable",
33
+ "Urease": "Variable",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Unknown",
36
+ "VP": "Unknown",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Unknown",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Variable",
42
+ "Esculin Hydrolysis": "Variable",
43
+ "Nitrate Reduction": "Variable",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Unknown",
47
+ "Ornithine Decarboxylase": "Unknown",
48
+ "Ornitihine Decarboxylase": "Unknown",
49
+ "Arginine dihydrolase": "Unknown",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Variable",
52
+ "Sucrose Fermentation": "Variable",
53
+ "Maltose Fermentation": "Variable",
54
+ "Mannitol Fermentation": "Variable",
55
+ "Sorbitol Fermentation": "Variable",
56
+ "Xylose Fermentation": "Variable",
57
+ "Rhamnose Fermentation": "Unknown",
58
+ "Arabinose Fermentation": "Variable",
59
+ "Raffinose Fermentation": "Unknown",
60
+ "Trehalose Fermentation": "Variable",
61
+ "Inositol Fermentation": "Unknown",
62
+ "Gas Production": "Variable",
63
+ "TSI Pattern": "Unknown",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "field_notes": {
70
+ "Oxygen Requirement": "Many Actinomyces are best recovered under anaerobic or microaerophilic conditions, but may tolerate oxygen depending on species and culture conditions.",
71
+ "Colony Morphology": "Colonies are often irregular and may appear rough or granular; prolonged incubation can accentuate characteristic appearances.",
72
+ "Catalase": "Typically catalase negative, helping distinguish from aerobic actinomycetes."
73
+ },
74
+
75
+ "key_differentiators": [
76
+ {
77
+ "field": "Gram Stain",
78
+ "expected": "Positive",
79
+ "distinguishes_from": ["Actinobacillus", "Aggregatibacter"],
80
+ "notes": "Gram-positive morphology separates Actinomyces from Gram-negative oral flora."
81
+ },
82
+ {
83
+ "field": "Motility",
84
+ "expected": "Negative",
85
+ "distinguishes_from": ["Bacillus", "Listeria"],
86
+ "notes": "Non-motility supports Actinomyces over motile Gram-positive rods."
87
+ },
88
+ {
89
+ "field": "Spore Formation",
90
+ "expected": "Negative",
91
+ "distinguishes_from": ["Bacillus", "Clostridium"],
92
+ "notes": "Non-spore forming supports Actinomyces in chronic abscess settings."
93
+ }
94
+ ],
95
+
96
+ "common_confusions": [
97
+ {
98
+ "genus": "Nocardia",
99
+ "reason": "Both can present as branching Gram-positive rods and cause chronic infections."
100
+ },
101
+ {
102
+ "genus": "Corynebacterium",
103
+ "reason": "Overlapping Gram-positive rod morphology may confuse if branching is not described."
104
+ }
105
+ ],
106
+
107
+ "when_to_question_identification": [
108
+ "Strong aerobic growth with catalase positivity suggests Nocardia or other aerobic actinomycetes.",
109
+ "Spore formation suggests Bacillus or Clostridium rather than Actinomyces.",
110
+ "Oxidase positivity argues against Actinomyces."
111
+ ],
112
+
113
+ "recommended_next_tests": [
114
+ {
115
+ "test": "Anaerobic incubation",
116
+ "reason": "Improves recovery and supports identification consistent with Actinomyces."
117
+ },
118
+ {
119
+ "test": "Acid fast",
120
+ "reason": "Helps distinguish Actinomyces (typically non–acid fast) from Nocardia (often partially acid fast)."
121
+ },
122
+ {
123
+ "test": "MALDI-TOF MS",
124
+ "reason": "Preferred for reliable genus/species identification due to phenotypic overlap."
125
+ }
126
+ ],
127
+
128
+ "supported_species": [
129
+ "israelii",
130
+ "naeslundii",
131
+ "viscosus",
132
+ "odontolyticus",
133
+ "meyeri"
134
+ ]
135
+ }
data/rag/knowledge_base/Actinomyces/israelii.json ADDED
@@ -0,0 +1,108 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Actinomyces",
5
+ "species": "israelii",
6
+
7
+ "overview": {
8
+ "short": "Actinomyces israelii is a Gram-positive, non-spore-forming, filamentous rod classically associated with actinomycosis.",
9
+ "clinical_context": "Most common cause of cervicofacial actinomycosis, often presenting with chronic abscesses and draining sinus tracts containing sulfur granules."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Positive",
14
+ "Shape": "Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "White",
25
+ "Grey",
26
+ "Rough",
27
+ "Irregular"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "30//37",
31
+ "Catalase": "Negative",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Unknown",
37
+ "VP": "Unknown",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Unknown",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Positive",
43
+ "Esculin Hydrolysis": "Variable",
44
+ "Nitrate Reduction": "Variable",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Unknown",
48
+ "Ornithine Decarboxylase": "Unknown",
49
+ "Ornitihine Decarboxylase": "Unknown",
50
+ "Arginine dihydrolase": "Unknown",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Variable",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Variable",
58
+ "Rhamnose Fermentation": "Unknown",
59
+ "Arabinose Fermentation": "Variable",
60
+ "Raffinose Fermentation": "Unknown",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Unknown",
63
+ "Gas Production": "Variable",
64
+ "TSI Pattern": "Unknown",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Gelatin Hydrolysis",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Consistent gelatin hydrolysis supports A. israelii."
76
+ },
77
+ {
78
+ "field": "Lactose Fermentation",
79
+ "value": "Negative",
80
+ "importance": "medium",
81
+ "notes": "Helps separate from oral Actinomyces species."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Actinomyces naeslundii",
88
+ "reason": "Shared oral habitat and overlapping anaerobic growth characteristics."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Catalase positivity suggests aerobic actinomycetes.",
94
+ "Strong aerobic growth argues against A. israelii.",
95
+ "Acid-fast positivity suggests Nocardia."
96
+ ],
97
+
98
+ "recommended_next_tests": [
99
+ {
100
+ "test": "Anaerobic culture",
101
+ "reason": "Required for optimal recovery and confirmation."
102
+ },
103
+ {
104
+ "test": "MALDI-TOF MS",
105
+ "reason": "Reliable species-level differentiation."
106
+ }
107
+ ]
108
+ }
data/rag/knowledge_base/Actinomyces/naeslundii.json ADDED
@@ -0,0 +1,106 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Actinomyces",
5
+ "species": "naeslundii",
6
+
7
+ "overview": {
8
+ "short": "Actinomyces naeslundii is a Gram-positive, non-spore-forming rod commonly found in the human oral cavity.",
9
+ "clinical_context": "Associated with dental plaque, root caries, and occasional invasive infections."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Positive",
14
+ "Shape": "Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "White",
25
+ "Grey",
26
+ "Smooth"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "30//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Variable",
33
+ "Urease": "Variable",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Unknown",
36
+ "VP": "Unknown",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Unknown",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Positive",
43
+ "Nitrate Reduction": "Positive",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Unknown",
47
+ "Ornithine Decarboxylase": "Unknown",
48
+ "Ornitihine Decarboxylase": "Unknown",
49
+ "Arginine dihydrolase": "Unknown",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Positive",
52
+ "Sucrose Fermentation": "Positive",
53
+ "Maltose Fermentation": "Positive",
54
+ "Mannitol Fermentation": "Variable",
55
+ "Sorbitol Fermentation": "Variable",
56
+ "Xylose Fermentation": "Variable",
57
+ "Rhamnose Fermentation": "Unknown",
58
+ "Arabinose Fermentation": "Variable",
59
+ "Raffinose Fermentation": "Unknown",
60
+ "Trehalose Fermentation": "Positive",
61
+ "Inositol Fermentation": "Unknown",
62
+ "Gas Production": "Variable",
63
+ "TSI Pattern": "Unknown",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Esculin Hydrolysis",
72
+ "value": "Positive",
73
+ "importance": "high",
74
+ "notes": "Useful discriminator among oral Actinomyces."
75
+ },
76
+ {
77
+ "field": "Lactose Fermentation",
78
+ "value": "Positive",
79
+ "importance": "medium",
80
+ "notes": "Helps differentiate from A. israelii."
81
+ }
82
+ ],
83
+
84
+ "common_confusions": [
85
+ {
86
+ "species": "Actinomyces odontolyticus",
87
+ "reason": "Both are oral species with overlapping sugar fermentation patterns."
88
+ }
89
+ ],
90
+
91
+ "when_to_question_identification": [
92
+ "Gelatin hydrolysis positivity suggests other Actinomyces species.",
93
+ "Strict anaerobiosis suggests A. israelii."
94
+ ],
95
+
96
+ "recommended_next_tests": [
97
+ {
98
+ "test": "Esculin hydrolysis",
99
+ "reason": "Key species-level discriminator."
100
+ },
101
+ {
102
+ "test": "MALDI-TOF MS",
103
+ "reason": "Accurate differentiation among oral Actinomyces."
104
+ }
105
+ ]
106
+ }
data/rag/knowledge_base/Actinomyces/odontolyticus.json ADDED
@@ -0,0 +1,106 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Actinomyces",
5
+ "species": "odontolyticus",
6
+
7
+ "overview": {
8
+ "short": "Actinomyces odontolyticus is a Gram-positive, non-spore-forming rod commonly isolated from dental plaque and oral infections.",
9
+ "clinical_context": "Frequently associated with dental caries, periodontal disease, and occasional systemic infections."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Positive",
14
+ "Shape": "Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "White",
25
+ "Grey",
26
+ "Smooth"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "30//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Positive",
33
+ "Urease": "Negative",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Unknown",
36
+ "VP": "Unknown",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Unknown",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Variable",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Unknown",
47
+ "Ornithine Decarboxylase": "Unknown",
48
+ "Ornitihine Decarboxylase": "Unknown",
49
+ "Arginine dihydrolase": "Unknown",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Positive",
52
+ "Sucrose Fermentation": "Positive",
53
+ "Maltose Fermentation": "Positive",
54
+ "Mannitol Fermentation": "Positive",
55
+ "Sorbitol Fermentation": "Variable",
56
+ "Xylose Fermentation": "Variable",
57
+ "Rhamnose Fermentation": "Unknown",
58
+ "Arabinose Fermentation": "Variable",
59
+ "Raffinose Fermentation": "Unknown",
60
+ "Trehalose Fermentation": "Positive",
61
+ "Inositol Fermentation": "Unknown",
62
+ "Gas Production": "Variable",
63
+ "TSI Pattern": "Unknown",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Indole",
72
+ "value": "Positive",
73
+ "importance": "high",
74
+ "notes": "Key differentiator from other common Actinomyces species."
75
+ },
76
+ {
77
+ "field": "Esculin Hydrolysis",
78
+ "value": "Negative",
79
+ "importance": "medium",
80
+ "notes": "Helps separate from A. naeslundii."
81
+ }
82
+ ],
83
+
84
+ "common_confusions": [
85
+ {
86
+ "species": "Actinomyces naeslundii",
87
+ "reason": "Overlapping oral habitat and sugar fermentation."
88
+ }
89
+ ],
90
+
91
+ "when_to_question_identification": [
92
+ "Indole negativity suggests other Actinomyces species.",
93
+ "Strong gelatin hydrolysis suggests A. israelii."
94
+ ],
95
+
96
+ "recommended_next_tests": [
97
+ {
98
+ "test": "Indole test",
99
+ "reason": "Primary discriminator for A. odontolyticus."
100
+ },
101
+ {
102
+ "test": "MALDI-TOF MS",
103
+ "reason": "Reliable species confirmation."
104
+ }
105
+ ]
106
+ }
data/rag/knowledge_base/Aerococcus/genus.json ADDED
@@ -0,0 +1,137 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Aerococcus",
5
+
6
+ "overview": {
7
+ "short": "Aerococcus species are Gram-positive cocci that often appear in clusters or tetrads and resemble streptococci or staphylococci on initial examination.",
8
+ "clinical_context": "Associated with urinary tract infections, bacteremia, endocarditis, and invasive infections, particularly in elderly or immunocompromised patients."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Positive",
13
+ "Shape": "Cocci",
14
+ "Motility": "Negative",
15
+ "Capsule": "Variable",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Variable",
18
+ "Haemolysis Type": "Variable",
19
+ "Media Grown On": [
20
+ "Blood Agar"
21
+ ],
22
+ "Colony Morphology": [
23
+ "Small",
24
+ "Grey",
25
+ "Alpha-haemolytic or Non-haemolytic"
26
+ ],
27
+ "Oxygen Requirement": "Facultative Anaerobe",
28
+ "Growth Temperature": "30//37",
29
+ "Catalase": "Negative",
30
+ "Oxidase": "Negative",
31
+ "Indole": "Negative",
32
+ "Urease": "Negative",
33
+ "Citrate": "Negative",
34
+ "Methyl Red": "Unknown",
35
+ "VP": "Unknown",
36
+ "H2S": "Negative",
37
+ "DNase": "Negative",
38
+ "ONPG": "Unknown",
39
+ "Coagulase": "Negative",
40
+ "Gelatin Hydrolysis": "Negative",
41
+ "Esculin Hydrolysis": "Negative",
42
+ "Nitrate Reduction": "Negative",
43
+ "NaCl Tolerant (>=6%)": "Negative",
44
+ "Lipase Test": "Negative",
45
+ "Lysine Decarboxylase": "Unknown",
46
+ "Ornithine Decarboxylase": "Unknown",
47
+ "Ornitihine Decarboxylase": "Unknown",
48
+ "Arginine dihydrolase": "Negative",
49
+ "Glucose Fermentation": "Positive",
50
+ "Lactose Fermentation": "Variable",
51
+ "Sucrose Fermentation": "Variable",
52
+ "Maltose Fermentation": "Variable",
53
+ "Mannitol Fermentation": "Negative",
54
+ "Sorbitol Fermentation": "Negative",
55
+ "Xylose Fermentation": "Negative",
56
+ "Rhamnose Fermentation": "Unknown",
57
+ "Arabinose Fermentation": "Negative",
58
+ "Raffinose Fermentation": "Unknown",
59
+ "Trehalose Fermentation": "Variable",
60
+ "Inositol Fermentation": "Negative",
61
+ "Gas Production": "Negative",
62
+ "TSI Pattern": "Unknown",
63
+ "Colony Pattern": "Unknown",
64
+ "Pigment": "None",
65
+ "Motility Type": "None"
66
+ },
67
+
68
+ "field_notes": {
69
+ "Catalase": "Typically catalase-negative, but weak or pseudo-positive reactions may occur.",
70
+ "Haemolysis": "Most species are alpha-haemolytic or non-haemolytic on blood agar.",
71
+ "Shape": "Often described as cocci in tetrads or clusters, which can mimic staphylococci."
72
+ },
73
+
74
+ "key_differentiators": [
75
+ {
76
+ "field": "Catalase",
77
+ "expected": "Negative",
78
+ "distinguishes_from": ["Staphylococcus"],
79
+ "notes": "Catalase negativity helps separate Aerococcus from staphylococci."
80
+ },
81
+ {
82
+ "field": "NaCl Tolerant (>=6%)",
83
+ "expected": "Negative",
84
+ "distinguishes_from": ["Enterococcus"],
85
+ "notes": "Lack of growth in high salt differentiates Aerococcus from enterococci."
86
+ },
87
+ {
88
+ "field": "Haemolysis",
89
+ "expected": "Variable",
90
+ "distinguishes_from": ["Streptococcus"],
91
+ "notes": "Haemolysis pattern combined with colony morphology aids differentiation."
92
+ }
93
+ ],
94
+
95
+ "common_confusions": [
96
+ {
97
+ "genus": "Streptococcus",
98
+ "reason": "Similar Gram-positive cocci morphology and haemolysis patterns."
99
+ },
100
+ {
101
+ "genus": "Enterococcus",
102
+ "reason": "Overlapping biochemical reactions in urinary isolates."
103
+ },
104
+ {
105
+ "genus": "Staphylococcus",
106
+ "reason": "Clustered cocci appearance on Gram stain may be misleading."
107
+ }
108
+ ],
109
+
110
+ "when_to_question_identification": [
111
+ "Catalase-positive reaction suggests Staphylococcus.",
112
+ "Growth in 6.5% NaCl suggests Enterococcus.",
113
+ "Beta-haemolysis with streptococcal morphology suggests Streptococcus."
114
+ ],
115
+
116
+ "recommended_next_tests": [
117
+ {
118
+ "test": "Catalase test (repeat)",
119
+ "reason": "Weak reactions may require confirmation."
120
+ },
121
+ {
122
+ "test": "NaCl tolerance (6.5%)",
123
+ "reason": "Useful for exclusion of Enterococcus."
124
+ },
125
+ {
126
+ "test": "MALDI-TOF MS",
127
+ "reason": "Preferred method for accurate genus and species identification."
128
+ }
129
+ ],
130
+
131
+ "supported_species": [
132
+ "urinae",
133
+ "viridans",
134
+ "sanguinicola",
135
+ "christensenii"
136
+ ]
137
+ }
data/rag/knowledge_base/Aerococcus/sanguinicola.json ADDED
@@ -0,0 +1,96 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aerococcus",
5
+ "species": "sanguinicola",
6
+
7
+ "overview": {
8
+ "short": "Aerococcus sanguinicola is a Gram-positive, catalase-negative coccus associated with bloodstream and urinary tract infections.",
9
+ "clinical_context": "Often isolated from bacteremia or invasive infections in elderly or hospitalized patients."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Positive",
14
+ "Shape": "Cocci",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Positive",
19
+ "Haemolysis Type": "Alpha",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Small",
25
+ "Grey",
26
+ "Alpha-haemolytic"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "30//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Negative",
33
+ "Urease": "Negative",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Unknown",
36
+ "VP": "Unknown",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Unknown",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Negative",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Unknown",
47
+ "Ornithine Decarboxylase": "Unknown",
48
+ "Ornitihine Decarboxylase": "Unknown",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Variable",
52
+ "Sucrose Fermentation": "Variable",
53
+ "Maltose Fermentation": "Variable",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Unknown",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Unknown",
60
+ "Trehalose Fermentation": "Variable",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "Unknown",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Clinical Source",
72
+ "value": "Bloodstream",
73
+ "importance": "high",
74
+ "notes": "More frequently isolated from blood cultures than other Aerococcus species."
75
+ }
76
+ ],
77
+
78
+ "common_confusions": [
79
+ {
80
+ "species": "Aerococcus urinae",
81
+ "reason": "Overlapping biochemical profile and haemolysis pattern."
82
+ }
83
+ ],
84
+
85
+ "when_to_question_identification": [
86
+ "UTI-only presentation suggests Aerococcus urinae.",
87
+ "Beta-haemolysis suggests Streptococcus."
88
+ ],
89
+
90
+ "recommended_next_tests": [
91
+ {
92
+ "test": "MALDI-TOF MS",
93
+ "reason": "Essential for distinguishing Aerococcus species."
94
+ }
95
+ ]
96
+ }
data/rag/knowledge_base/Aerococcus/urinae.json ADDED
@@ -0,0 +1,111 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aerococcus",
5
+ "species": "urinae",
6
+
7
+ "overview": {
8
+ "short": "Aerococcus urinae is a Gram-positive, catalase-negative coccus commonly isolated from urinary tract infections.",
9
+ "clinical_context": "Frequently associated with UTIs, bacteremia, and infective endocarditis in elderly patients."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Positive",
14
+ "Shape": "Cocci",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Positive",
19
+ "Haemolysis Type": "Alpha",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Small",
25
+ "Grey",
26
+ "Alpha-haemolytic"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "30//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Negative",
33
+ "Urease": "Negative",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Unknown",
36
+ "VP": "Unknown",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Unknown",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Negative",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Unknown",
47
+ "Ornithine Decarboxylase": "Unknown",
48
+ "Ornitihine Decarboxylase": "Unknown",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Variable",
52
+ "Sucrose Fermentation": "Variable",
53
+ "Maltose Fermentation": "Variable",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Unknown",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Unknown",
60
+ "Trehalose Fermentation": "Variable",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "Unknown",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Clinical Source",
72
+ "value": "Urinary tract",
73
+ "importance": "high",
74
+ "notes": "Strong association with urinary isolates."
75
+ },
76
+ {
77
+ "field": "Haemolysis Type",
78
+ "value": "Alpha",
79
+ "importance": "medium",
80
+ "notes": "Typically alpha-haemolytic on blood agar."
81
+ }
82
+ ],
83
+
84
+ "common_confusions": [
85
+ {
86
+ "species": "Aerococcus sanguinicola",
87
+ "reason": "Similar biochemical profile and haemolysis pattern."
88
+ },
89
+ {
90
+ "genus": "Enterococcus",
91
+ "reason": "Shared UTI association and Gram-positive cocci morphology."
92
+ }
93
+ ],
94
+
95
+ "when_to_question_identification": [
96
+ "Growth in 6.5% NaCl suggests Enterococcus.",
97
+ "Catalase positivity suggests Staphylococcus.",
98
+ "Beta-haemolysis suggests Streptococcus."
99
+ ],
100
+
101
+ "recommended_next_tests": [
102
+ {
103
+ "test": "MALDI-TOF MS",
104
+ "reason": "Gold standard for distinguishing Aerococcus species."
105
+ },
106
+ {
107
+ "test": "16S rRNA sequencing",
108
+ "reason": "Useful when MALDI-TOF is inconclusive."
109
+ }
110
+ ]
111
+ }
data/rag/knowledge_base/Aerococcus/viridans.json ADDED
@@ -0,0 +1,96 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aerococcus",
5
+ "species": "viridans",
6
+
7
+ "overview": {
8
+ "short": "Aerococcus viridans is a Gram-positive, catalase-negative coccus historically associated with environmental and opportunistic infections.",
9
+ "clinical_context": "Less frequently isolated than other Aerococcus species; may be recovered from blood or wound cultures."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Positive",
14
+ "Shape": "Cocci",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Variable",
19
+ "Haemolysis Type": "Alpha",
20
+ "Media Grown On": [
21
+ "Blood Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Small",
25
+ "Grey",
26
+ "Alpha-haemolytic"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "30//37",
30
+ "Catalase": "Negative",
31
+ "Oxidase": "Negative",
32
+ "Indole": "Negative",
33
+ "Urease": "Negative",
34
+ "Citrate": "Negative",
35
+ "Methyl Red": "Unknown",
36
+ "VP": "Unknown",
37
+ "H2S": "Negative",
38
+ "DNase": "Negative",
39
+ "ONPG": "Unknown",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Negative",
42
+ "Esculin Hydrolysis": "Negative",
43
+ "Nitrate Reduction": "Negative",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Negative",
46
+ "Lysine Decarboxylase": "Unknown",
47
+ "Ornithine Decarboxylase": "Unknown",
48
+ "Ornitihine Decarboxylase": "Unknown",
49
+ "Arginine dihydrolase": "Negative",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Variable",
52
+ "Sucrose Fermentation": "Variable",
53
+ "Maltose Fermentation": "Variable",
54
+ "Mannitol Fermentation": "Negative",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Unknown",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Unknown",
60
+ "Trehalose Fermentation": "Variable",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Negative",
63
+ "TSI Pattern": "Unknown",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "None"
67
+ },
68
+
69
+ "species_markers": [
70
+ {
71
+ "field": "Clinical Relevance",
72
+ "value": "Lower",
73
+ "importance": "medium",
74
+ "notes": "Less commonly implicated in invasive disease."
75
+ }
76
+ ],
77
+
78
+ "common_confusions": [
79
+ {
80
+ "genus": "Streptococcus",
81
+ "reason": "Alpha-haemolytic colonies may mimic viridans streptococci."
82
+ }
83
+ ],
84
+
85
+ "when_to_question_identification": [
86
+ "Strong clinical UTI association suggests Aerococcus urinae.",
87
+ "Growth in high salt suggests Enterococcus."
88
+ ],
89
+
90
+ "recommended_next_tests": [
91
+ {
92
+ "test": "MALDI-TOF MS",
93
+ "reason": "Required for reliable species-level identification."
94
+ }
95
+ ]
96
+ }
data/rag/knowledge_base/Aeromonas/caviae.json ADDED
@@ -0,0 +1,122 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aeromonas",
5
+ "species": "caviae",
6
+
7
+ "overview": {
8
+ "short": "Aeromonas caviae is a Gram-negative, oxidase-positive, facultatively anaerobic rod associated mainly with gastrointestinal disease and occasional opportunistic infections.",
9
+ "clinical_context": "Often linked to gastroenteritis; may also be isolated from wounds and bloodstream infections in immunocompromised patients."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Large",
26
+ "Grey",
27
+ "Opaque"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "4//42",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Positive",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Positive",
40
+ "ONPG": "Positive",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Variable",
43
+ "Esculin Hydrolysis": "Variable",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Variable",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Positive",
49
+ "Ornitihine Decarboxylase": "Positive",
50
+ "Arginine dihydrolase": "Positive",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Positive",
54
+ "Maltose Fermentation": "Positive",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Variable",
64
+ "TSI Pattern": "A/A",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Indole",
73
+ "value": "Negative",
74
+ "importance": "high",
75
+ "notes": "Supports A. caviae over indole-positive Aeromonas such as A. veronii (often positive)."
76
+ },
77
+ {
78
+ "field": "Ornithine Decarboxylase",
79
+ "value": "Positive",
80
+ "importance": "high",
81
+ "notes": "Ornithine positivity is commonly used to separate A. caviae from A. hydrophila."
82
+ },
83
+ {
84
+ "field": "Lysine Decarboxylase",
85
+ "value": "Negative",
86
+ "importance": "medium",
87
+ "notes": "Helps distinguish A. caviae from lysine-positive Aeromonas patterns."
88
+ }
89
+ ],
90
+
91
+ "common_confusions": [
92
+ {
93
+ "species": "Aeromonas hydrophila",
94
+ "reason": "Overlapping oxidase-positive fermenter profile; separation relies on decarboxylase patterns and haemolysis."
95
+ },
96
+ {
97
+ "species": "Aeromonas veronii",
98
+ "reason": "Biochemically close; indole and ornithine patterns help resolve."
99
+ }
100
+ ],
101
+
102
+ "when_to_question_identification": [
103
+ "Indole positivity suggests A. veronii or another Aeromonas species.",
104
+ "Strong beta haemolysis may suggest A. hydrophila.",
105
+ "NaCl tolerance at >=6% suggests Vibrio rather than Aeromonas."
106
+ ],
107
+
108
+ "recommended_next_tests": [
109
+ {
110
+ "test": "Indole test",
111
+ "reason": "Key discriminator within Aeromonas."
112
+ },
113
+ {
114
+ "test": "Ornithine decarboxylase",
115
+ "reason": "Useful to support A. caviae identification."
116
+ },
117
+ {
118
+ "test": "MALDI-TOF MS",
119
+ "reason": "Recommended due to biochemical overlap within Aeromonas."
120
+ }
121
+ ]
122
+ }
data/rag/knowledge_base/Aeromonas/genus.json ADDED
@@ -0,0 +1,138 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "genus",
4
+ "genus": "Aeromonas",
5
+
6
+ "overview": {
7
+ "short": "Aeromonas species are Gram-negative, facultatively anaerobic rods commonly found in aquatic environments and associated with gastrointestinal and wound infections.",
8
+ "clinical_context": "Frequently implicated in gastroenteritis, wound infections following water exposure, and opportunistic bloodstream infections."
9
+ },
10
+
11
+ "expected_fields": {
12
+ "Gram Stain": "Negative",
13
+ "Shape": "Rods",
14
+ "Motility": "Positive",
15
+ "Capsule": "Variable",
16
+ "Spore Formation": "Negative",
17
+ "Haemolysis": "Variable",
18
+ "Haemolysis Type": "Variable",
19
+ "Media Grown On": [
20
+ "Blood Agar",
21
+ "MacConkey Agar"
22
+ ],
23
+ "Colony Morphology": [
24
+ "Large",
25
+ "Grey",
26
+ "Opaque"
27
+ ],
28
+ "Oxygen Requirement": "Facultative Anaerobe",
29
+ "Growth Temperature": "4//42",
30
+ "Catalase": "Positive",
31
+ "Oxidase": "Positive",
32
+ "Indole": "Variable",
33
+ "Urease": "Negative",
34
+ "Citrate": "Variable",
35
+ "Methyl Red": "Positive",
36
+ "VP": "Negative",
37
+ "H2S": "Negative",
38
+ "DNase": "Positive",
39
+ "ONPG": "Positive",
40
+ "Coagulase": "Negative",
41
+ "Gelatin Hydrolysis": "Positive",
42
+ "Esculin Hydrolysis": "Variable",
43
+ "Nitrate Reduction": "Positive",
44
+ "NaCl Tolerant (>=6%)": "Negative",
45
+ "Lipase Test": "Positive",
46
+ "Lysine Decarboxylase": "Variable",
47
+ "Ornithine Decarboxylase": "Variable",
48
+ "Ornitihine Decarboxylase": "Variable",
49
+ "Arginine dihydrolase": "Positive",
50
+ "Glucose Fermentation": "Positive",
51
+ "Lactose Fermentation": "Negative",
52
+ "Sucrose Fermentation": "Variable",
53
+ "Maltose Fermentation": "Positive",
54
+ "Mannitol Fermentation": "Variable",
55
+ "Sorbitol Fermentation": "Negative",
56
+ "Xylose Fermentation": "Negative",
57
+ "Rhamnose Fermentation": "Negative",
58
+ "Arabinose Fermentation": "Negative",
59
+ "Raffinose Fermentation": "Negative",
60
+ "Trehalose Fermentation": "Variable",
61
+ "Inositol Fermentation": "Negative",
62
+ "Gas Production": "Variable",
63
+ "TSI Pattern": "A/A",
64
+ "Colony Pattern": "Unknown",
65
+ "Pigment": "None",
66
+ "Motility Type": "Polar"
67
+ },
68
+
69
+ "field_notes": {
70
+ "Oxidase": "Oxidase positivity is a key distinguishing feature from Enterobacterales.",
71
+ "Motility": "Typically motile by polar flagella.",
72
+ "Lactose Fermentation": "Generally non-lactose fermenting on MacConkey Agar."
73
+ },
74
+
75
+ "key_differentiators": [
76
+ {
77
+ "field": "Oxidase",
78
+ "expected": "Positive",
79
+ "distinguishes_from": ["Enterobacter", "Escherichia", "Citrobacter"],
80
+ "notes": "Separates Aeromonas from most Enterobacterales."
81
+ },
82
+ {
83
+ "field": "DNase",
84
+ "expected": "Positive",
85
+ "distinguishes_from": ["Vibrio"],
86
+ "notes": "DNase positivity supports Aeromonas over Vibrio."
87
+ },
88
+ {
89
+ "field": "NaCl Tolerant (>=6%)",
90
+ "expected": "Negative",
91
+ "distinguishes_from": ["Vibrio"],
92
+ "notes": "Lack of salt tolerance differentiates Aeromonas from halophilic vibrios."
93
+ }
94
+ ],
95
+
96
+ "common_confusions": [
97
+ {
98
+ "genus": "Vibrio",
99
+ "reason": "Shared oxidase positivity and aquatic association."
100
+ },
101
+ {
102
+ "genus": "Plesiomonas",
103
+ "reason": "Overlapping biochemical reactions and motility."
104
+ },
105
+ {
106
+ "genus": "Enterobacter",
107
+ "reason": "Shared glucose fermentation and colony appearance on non-selective media."
108
+ }
109
+ ],
110
+
111
+ "when_to_question_identification": [
112
+ "Growth in high salt suggests Vibrio.",
113
+ "Oxidase negativity argues against Aeromonas.",
114
+ "Strong lactose fermentation suggests Enterobacterales."
115
+ ],
116
+
117
+ "recommended_next_tests": [
118
+ {
119
+ "test": "Oxidase test",
120
+ "reason": "Critical for initial differentiation from Enterobacterales."
121
+ },
122
+ {
123
+ "test": "Salt tolerance testing",
124
+ "reason": "Helps distinguish from Vibrio species."
125
+ },
126
+ {
127
+ "test": "MALDI-TOF MS",
128
+ "reason": "Recommended for accurate species-level identification."
129
+ }
130
+ ],
131
+
132
+ "supported_species": [
133
+ "hydrophila",
134
+ "caviae",
135
+ "veronii",
136
+ "sobria"
137
+ ]
138
+ }
data/rag/knowledge_base/Aeromonas/hydrophila.json ADDED
@@ -0,0 +1,122 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aeromonas",
5
+ "species": "hydrophila",
6
+
7
+ "overview": {
8
+ "short": "Aeromonas hydrophila is a Gram-negative, oxidase-positive, facultatively anaerobic rod frequently associated with wound infections and gastroenteritis, and can cause invasive disease.",
9
+ "clinical_context": "Often linked to water-exposure wound infections, diarrheal disease, and opportunistic septicemia."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Positive",
19
+ "Haemolysis Type": "Beta",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Large",
26
+ "Grey",
27
+ "Opaque"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "4//42",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Variable",
34
+ "Urease": "Negative",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Positive",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Positive",
40
+ "ONPG": "Positive",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Positive",
43
+ "Esculin Hydrolysis": "Variable",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Positive",
47
+ "Lysine Decarboxylase": "Positive",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Positive",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Positive",
55
+ "Mannitol Fermentation": "Positive",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Variable",
64
+ "TSI Pattern": "A/A",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Haemolysis Type",
73
+ "value": "Beta",
74
+ "importance": "high",
75
+ "notes": "Beta haemolysis is more supportive of A. hydrophila compared with A. caviae (often non-haemolytic)."
76
+ },
77
+ {
78
+ "field": "Gelatin Hydrolysis",
79
+ "value": "Positive",
80
+ "importance": "high",
81
+ "notes": "Gelatinase positivity is commonly used in Aeromonas differentiation and supports A. hydrophila."
82
+ },
83
+ {
84
+ "field": "Ornithine Decarboxylase",
85
+ "value": "Negative",
86
+ "importance": "medium",
87
+ "notes": "Helps separate from A. caviae, which is more often ornithine positive."
88
+ }
89
+ ],
90
+
91
+ "common_confusions": [
92
+ {
93
+ "species": "Aeromonas veronii",
94
+ "reason": "Overlap in oxidase-positive fermentation pattern; indole and haemolysis patterns are helpful."
95
+ },
96
+ {
97
+ "species": "Aeromonas caviae",
98
+ "reason": "Both can present in gastroenteritis; ornithine and haemolysis help distinguish."
99
+ }
100
+ ],
101
+
102
+ "when_to_question_identification": [
103
+ "Consistent non-haemolysis suggests A. caviae or another Aeromonas species.",
104
+ "Strong indole positivity suggests A. veronii or related taxa.",
105
+ "NaCl tolerance at >=6% suggests Vibrio rather than Aeromonas."
106
+ ],
107
+
108
+ "recommended_next_tests": [
109
+ {
110
+ "test": "Haemolysis on Blood Agar",
111
+ "reason": "Supports species-level discrimination inside Aeromonas."
112
+ },
113
+ {
114
+ "test": "Gelatin hydrolysis",
115
+ "reason": "Commonly positive and useful for A. hydrophila support."
116
+ },
117
+ {
118
+ "test": "MALDI-TOF MS",
119
+ "reason": "Recommended for accurate differentiation among Aeromonas species."
120
+ }
121
+ ]
122
+ }
data/rag/knowledge_base/Aeromonas/veronii.json ADDED
@@ -0,0 +1,122 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aeromonas",
5
+ "species": "veronii",
6
+
7
+ "overview": {
8
+ "short": "Aeromonas veronii is a Gram-negative, oxidase-positive, facultatively anaerobic rod associated with gastrointestinal illness and opportunistic infections.",
9
+ "clinical_context": "Often isolated from diarrheal disease and can cause wound or bloodstream infections, especially in immunocompromised hosts."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Rods",
15
+ "Motility": "Positive",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Variable",
19
+ "Haemolysis Type": "Variable",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "MacConkey Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Large",
26
+ "Grey",
27
+ "Opaque"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "4//42",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Positive",
33
+ "Indole": "Positive",
34
+ "Urease": "Negative",
35
+ "Citrate": "Variable",
36
+ "Methyl Red": "Positive",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Positive",
40
+ "ONPG": "Positive",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Variable",
43
+ "Esculin Hydrolysis": "Variable",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Variable",
47
+ "Lysine Decarboxylase": "Variable",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Positive",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Positive",
55
+ "Mannitol Fermentation": "Variable",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Variable",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Variable",
64
+ "TSI Pattern": "A/A",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "Polar"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Indole",
73
+ "value": "Positive",
74
+ "importance": "high",
75
+ "notes": "Indole positivity strongly supports A. veronii over A. caviae (often indole negative)."
76
+ },
77
+ {
78
+ "field": "Ornithine Decarboxylase",
79
+ "value": "Negative",
80
+ "importance": "medium",
81
+ "notes": "Helps separate from A. caviae, which is more often ornithine positive."
82
+ },
83
+ {
84
+ "field": "Haemolysis",
85
+ "value": "Variable",
86
+ "importance": "medium",
87
+ "notes": "Haemolysis may occur but is less consistently defining than in A. hydrophila."
88
+ }
89
+ ],
90
+
91
+ "common_confusions": [
92
+ {
93
+ "species": "Aeromonas hydrophila",
94
+ "reason": "Overlap in oxidase-positive fermentation and gelatinase patterns; haemolysis and marker patterns help resolve."
95
+ },
96
+ {
97
+ "species": "Aeromonas caviae",
98
+ "reason": "Both associated with gastroenteritis; indole and ornithine are useful differentiators."
99
+ }
100
+ ],
101
+
102
+ "when_to_question_identification": [
103
+ "Indole negativity suggests A. caviae or another Aeromonas species.",
104
+ "Strong consistent beta haemolysis suggests A. hydrophila.",
105
+ "NaCl tolerance at >=6% suggests Vibrio rather than Aeromonas."
106
+ ],
107
+
108
+ "recommended_next_tests": [
109
+ {
110
+ "test": "Indole test",
111
+ "reason": "Primary discriminator for A. veronii support."
112
+ },
113
+ {
114
+ "test": "Ornithine decarboxylase",
115
+ "reason": "Supports separation from A. caviae."
116
+ },
117
+ {
118
+ "test": "MALDI-TOF MS",
119
+ "reason": "Recommended for definitive Aeromonas species identification."
120
+ }
121
+ ]
122
+ }
data/rag/knowledge_base/Aggregatibacter/actinomycetemcomitans.json ADDED
@@ -0,0 +1,108 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aggregatibacter",
5
+ "species": "actinomycetemcomitans",
6
+
7
+ "overview": {
8
+ "short": "Aggregatibacter actinomycetemcomitans is a fastidious Gram-negative coccobacillus associated with periodontal disease and infective endocarditis.",
9
+ "clinical_context": "Strongly linked to aggressive periodontitis and is a recognized HACEK organism causing endocarditis."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Short Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Variable",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Chocolate Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Small",
26
+ "Rough",
27
+ "Star-shaped center"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "35//37",
31
+ "Catalase": "Positive",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Positive",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Negative",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "Unknown",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Colony Morphology",
73
+ "value": "Star-shaped center",
74
+ "importance": "high",
75
+ "notes": "Characteristic star-shaped colonies are strongly suggestive of A. actinomycetemcomitans."
76
+ },
77
+ {
78
+ "field": "Catalase",
79
+ "value": "Positive",
80
+ "importance": "medium",
81
+ "notes": "Helps distinguish from other Aggregatibacter species."
82
+ }
83
+ ],
84
+
85
+ "common_confusions": [
86
+ {
87
+ "species": "Aggregatibacter aphrophilus",
88
+ "reason": "Similar fastidious growth and biochemical profile."
89
+ }
90
+ ],
91
+
92
+ "when_to_question_identification": [
93
+ "Absence of star-shaped colony morphology.",
94
+ "Oxidase positivity suggests another genus.",
95
+ "Robust growth on MacConkey Agar is inconsistent."
96
+ ],
97
+
98
+ "recommended_next_tests": [
99
+ {
100
+ "test": "Extended incubation",
101
+ "reason": "Characteristic colony morphology may take several days to develop."
102
+ },
103
+ {
104
+ "test": "MALDI-TOF MS",
105
+ "reason": "Reliable identification among HACEK organisms."
106
+ }
107
+ ]
108
+ }
data/rag/knowledge_base/Aggregatibacter/aphrophilus.json ADDED
@@ -0,0 +1,102 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "schema_version": "1.0",
3
+ "level": "species",
4
+ "genus": "Aggregatibacter",
5
+ "species": "aphrophilus",
6
+
7
+ "overview": {
8
+ "short": "Aggregatibacter aphrophilus is a Gram-negative, fastidious coccobacillus commonly isolated from the oral cavity and associated with endocarditis.",
9
+ "clinical_context": "A member of the HACEK group, frequently implicated in culture-negative endocarditis."
10
+ },
11
+
12
+ "expected_fields": {
13
+ "Gram Stain": "Negative",
14
+ "Shape": "Short Rods",
15
+ "Motility": "Negative",
16
+ "Capsule": "Negative",
17
+ "Spore Formation": "Negative",
18
+ "Haemolysis": "Negative",
19
+ "Haemolysis Type": "None",
20
+ "Media Grown On": [
21
+ "Blood Agar",
22
+ "Chocolate Agar"
23
+ ],
24
+ "Colony Morphology": [
25
+ "Small",
26
+ "Smooth",
27
+ "Grey"
28
+ ],
29
+ "Oxygen Requirement": "Facultative Anaerobe",
30
+ "Growth Temperature": "35//37",
31
+ "Catalase": "Negative",
32
+ "Oxidase": "Negative",
33
+ "Indole": "Negative",
34
+ "Urease": "Negative",
35
+ "Citrate": "Negative",
36
+ "Methyl Red": "Negative",
37
+ "VP": "Negative",
38
+ "H2S": "Negative",
39
+ "DNase": "Negative",
40
+ "ONPG": "Negative",
41
+ "Coagulase": "Negative",
42
+ "Gelatin Hydrolysis": "Negative",
43
+ "Esculin Hydrolysis": "Negative",
44
+ "Nitrate Reduction": "Negative",
45
+ "NaCl Tolerant (>=6%)": "Negative",
46
+ "Lipase Test": "Negative",
47
+ "Lysine Decarboxylase": "Negative",
48
+ "Ornithine Decarboxylase": "Negative",
49
+ "Ornitihine Decarboxylase": "Negative",
50
+ "Arginine dihydrolase": "Negative",
51
+ "Glucose Fermentation": "Positive",
52
+ "Lactose Fermentation": "Negative",
53
+ "Sucrose Fermentation": "Variable",
54
+ "Maltose Fermentation": "Negative",
55
+ "Mannitol Fermentation": "Negative",
56
+ "Sorbitol Fermentation": "Negative",
57
+ "Xylose Fermentation": "Negative",
58
+ "Rhamnose Fermentation": "Negative",
59
+ "Arabinose Fermentation": "Negative",
60
+ "Raffinose Fermentation": "Negative",
61
+ "Trehalose Fermentation": "Negative",
62
+ "Inositol Fermentation": "Negative",
63
+ "Gas Production": "Negative",
64
+ "TSI Pattern": "Unknown",
65
+ "Colony Pattern": "Unknown",
66
+ "Pigment": "None",
67
+ "Motility Type": "None"
68
+ },
69
+
70
+ "species_markers": [
71
+ {
72
+ "field": "Catalase",
73
+ "value": "Negative",
74
+ "importance": "high",
75
+ "notes": "Differentiates A. aphrophilus from A. actinomycetemcomitans."
76
+ }
77
+ ],
78
+
79
+ "common_confusions": [
80
+ {
81
+ "species": "Aggregatibacter actinomycetemcomitans",
82
+ "reason": "Shared habitat and similar growth characteristics."
83
+ }
84
+ ],
85
+
86
+ "when_to_question_identification": [
87
+ "Catalase positivity suggests A. actinomycetemcomitans.",
88
+ "Star-shaped colonies suggest A. actinomycetemcomitans.",
89
+ "Growth on MacConkey Agar argues against Aggregatibacter."
90
+ ],
91
+
92
+ "recommended_next_tests": [
93
+ {
94
+ "test": "Catalase test",
95
+ "reason": "Key discriminator within Aggregatibacter species."
96
+ },
97
+ {
98
+ "test": "MALDI-TOF MS",
99
+ "reason": "Accurate identification of HACEK organisms."
100
+ }
101
+ ]
102
+ }