The microbiologyevents table

Table source: Hospital database.

Table purpose: Contains microbiology information, including cultures acquired and associated sensitivities.

Number of rows: 631,726

Links to:

  • PATIENTS on SUBJECT_ID
  • ADMISSIONS on HADM_ID
  • D_ITEMS on SPEC_ITEMID
  • D_ITEMS on ORG_ITEMID
  • D_ITEMS on AB_ITEMID

Important considerations

  • If the organism is null, then the culture had no growth reported.
  • In the source data for MIMIC there is a distinct column that describes the test performed, which is not included in MIMIC-III.
  • Individual rows corresponding to the type of test ordered are not included in MIMIC-III. Examples of this would be a row only describing the type of test e.g. “anaerobic bottle”, “aerobic bottle”, etc
  • Store time is not available. Blood cultures generally take days to complete, and the charttime should be considered as when the culture was relevant, not when it was available to patients.

Table columns

Name Postgres data type
ROW_ID INT
SUBJECT_ID INT
HADM_ID INT
CHARTDATE TIMESTAMP(0)
CHARTTIME TIMESTAMP(0)
SPEC_ITEMID INT
SPEC_TYPE_DESC VARCHAR(100)
ORG_ITEMID INT
ORG_NAME VARCHAR(100)
ISOLATE_NUM SMALLINT
AB_ITEMID INT
AB_NAME VARCHAR(30)
DILUTION_TEXT VARCHAR(10)
DILUTION_COMPARISON VARCHAR(20)
DILUTION_VALUE DOUBLE PRECISION
INTERPRETATION VARCHAR(5)

Detailed Description

SUBJECT_ID, HADM_ID

Identifiers which specify the patient: SUBJECT_ID is unique to a patient and HADM_ID is unique to a patient hospital stay.

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

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

ORG_ITEMID, ORG_NAME

The organism, if any, which grew when tested. If NULL, no organism grew (i.e. 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 name 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.

MIMIC-III v1.4 documentation