microbiologyevents

Hospital level table

microbiologyevents

Microbiology tests are a common procedure to check for infectious growth and to assess which antibiotic treatments are most effective.

The table is best explained with a demonstrative example. If a blood culture is requested for a patient, then a blood sample will be taken and sent to the microbiology lab. The time at which this blood sample is taken is the charttime. The spec_type_desc will indicate that this is a blood sample. Bacteria will be cultured on the blood sample, and the remaining columns depend on the outcome of this growth:

  • If no growth is found, the remaining columns will be NULL
  • If bacteria is found, then each organism of bacteria will be present in org_name, resulting in multiple rows for the single specimen (i.e. multiple rows for the given spec_type_desc).
  • If antibiotics are tested on a given bacterial organism, then each antibiotic tested will be present in the ab_name column (i.e. multiple rows for the given org_name associated with the given spec_type_desc). Antibiotic parameters and sensitivities are present in the remaining columns (dilution_text, dilution_comparison, dilution_value, interpretation).
  • d_micro on spec_itemid
  • d_micro on test_itemid
  • d_micro on org_itemid
  • d_micro on ab_itemid

Table columns

Name Postgres data type
subject_id INTEGER
hadm_id INTEGER
stay_id INTEGER
spec_id VARCHAR(8) NOT NULL
chartdate TIMESTAMP(0) NOT NULL
charttime TIMESTAMP(0)
spec_itemid INTEGER NOT NULL
spec_type_desc VARCHAR(100) NOT NULL
test_seq INTEGER NOT NULL
storedate TIMESTAMP(0)
storetime TIMESTAMP(0)
test_itemid INTEGER
test_name VARCHAR(100)
test_text VARCHAR
org_itemid INTEGER
org_name VARCHAR(100)
isolate_num SMALLINT
quantity VARCHAR(50)
ab_itemid INTEGER
ab_name VARCHAR(30)
dilution_text VARCHAR(10)
dilution_comparison VARCHAR(20)
dilution_value DOUBLE PRECISION
interpretation VARCHAR(5)

subject_id

subject_id is a unique identifier which specifies an individual patient. Any rows associated with a single subject_id pertain to the same individual.

hadm_id

hadm_id is an integer identifier which is unique for each patient hospitalization.


Last modified August 14, 2020: update website to use docsy (adc506c)