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
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
- If antibiotics are tested on a given bacterial organism, then each antibiotic tested will be present in the
ab_namecolumn (i.e. multiple rows for the given
org_nameassociated with the given
spec_type_desc). Antibiotic parameters and sensitivities are present in the remaining columns (
|Name||Postgres data type||Example value|
||INTEGER NOT NULL||1234567|
||INTEGER NOT NULL||6386644|
||TIMESTAMP(0) NOT NULL||2130-04-01 00:00:00|
||INTEGER NOT NULL||70012|
||VARCHAR(100) NOT NULL||BLOOD CULTURE|
||INTEGER NOT NULL||2|
||VARCHAR(100)||STAPHYLOCOCCUS, COAGULASE NEGATIVE|
A unique integer denoting the row.
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 is an integer identifier which is unique for each patient hospitalization.
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
chartdate is equal to a truncated version of
charttime without the timing information). Not all observations have a
charttime, but all observations have a
The specimen which is tested for bacterial growth. The specimen is a sample derived from a patient; e.g. blood, urine, sputum, etc.
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).
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.
The test performed on the given specimen.
The organism, if any, which grew when tested. If NULL, no organism grew (i.e. a negative culture).
For testing antibiotics, the isolated colony (integer; starts at 1).
If an antibiotic was tested against the given organism for sensitivity, the antibiotic is listed here.
Dilution values when testing antibiotic sensitivity.
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.
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:
NULL comment indicates no comment was made for the row.
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