microbiologyevents

Microbiology cultures.

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).

Table columns

Name Postgres data type Example value
microevent_id INTEGER NOT NULL 1234567
subject_id INTEGER 12078372
hadm_id INTEGER 29450599
micro_specimen_id INTEGER NOT NULL 6386644
chartdate TIMESTAMP(0) NOT NULL 2130-04-01 00:00:00
charttime TIMESTAMP(0) 2130-04-01 16:00:00
spec_itemid INTEGER NOT NULL 70012
spec_type_desc VARCHAR(100) NOT NULL BLOOD CULTURE
test_seq INTEGER NOT NULL 2
storedate TIMESTAMP(0) 2130-04-05 00:00:00
storetime TIMESTAMP(0) 2130-04-05 14:46:00
test_itemid INTEGER 90117
test_name VARCHAR(100) ANAEROBIC BOTTLE
org_itemid INTEGER 80155
org_name VARCHAR(100) STAPHYLOCOCCUS, COAGULASE NEGATIVE
isolate_num SMALLINT 1
quantity VARCHAR(50)
ab_itemid INTEGER 90025
ab_name VARCHAR(30) LEVOFLOXACIN
dilution_text VARCHAR(10) <=0.12
dilution_comparison VARCHAR(20) <=
dilution_value DOUBLE PRECISION 0.12
interpretation VARCHAR(5) S
comments TEXT ___

microevent_id

A unique integer denoting the row.

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.

chartdate, charttime

charttime records the time at which an observation was charted, and is usually the closest proxy to the time the data was actually measured. chartdate is the same as charttime, except there is no time available.

chartdate was included as time information is not always available for microbiology measurements: in order to be clear about when this occurs, charttime is null, and chartdate contains the date of the measurement.

In the cases where both charttime and chartdate exists, chartdate is equal to a truncated version of charttime (i.e. charttime without the timing information). Not all observations have a charttime, but all observations have a chartdate.

spec_itemid, spec_type_desc

The specimen which is tested for bacterial growth. The specimen is a sample derived from a patient; e.g. blood, urine, sputum, etc.

test_seq

If multiple samples are drawn, the test_seq will delineate them. For example, if an aerobic and anerobic culture bottle are used for the same specimen, they will have distinct test_seq values (likely 1 and 2).

storedate, storetime

The date (storedate) or date and time (storetime) of when the microbiology result was available. While many interim results are made available during the process of assessing a microbiology culture, the times here are the time of the last known update.

test_itemid, test_name

The test performed on the given specimen.

org_itemid, org_name

The organism, if any, which grew when tested. If NULL, no organism grew (i.e. a negative culture).

isolate_num

For testing antibiotics, the isolated colony (integer; starts at 1).

ab_itemid, ab_name

If an antibiotic was tested against the given organism for sensitivity, the antibiotic is listed here.

dilution_text, dilution_comparison, dilution_value

Dilution values when testing antibiotic sensitivity.

interpretation

interpretation of the antibiotic sensitivity, and indicates the results of the test. “S” is sensitive, “R” is resistant, “I” is intermediate, and “P” is pending.

comments

Deidentified free-text comments associated with the microbiology measurement. Usually these provide information about the sample, whether any notifications were made to care providers regarding the results, considerations for interpretation, or in some cases the comments contain the result of the measurement itself. Comments which have been fully deidentified (i.e. no information content retained) are present as three underscores: ___. A NULL comment indicates no comment was made for the row.