microbiologyevents

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).

Important considerations

Typically, negative values are indicated by a NULL value. However, itemid 90856 has a value of “NEGATIVE”, and should be included in queries which seek to segregate microbiology data based on positive/negative findings.

hadm_id is assigned to observations using the administrative transfer table. However this does not always perfectly capture labs around the hospital stay. To be specific, as of v2.1, it is possible to assign 1,449,547 observations with an hadm_id using a join to admissions with subject_id, admittime, and dischtime. However, only 1,396,224 (96%) of these observations have an hadm_id actually stored in the microbiologyevents table. Users wishing to ensure capture of labs proximal to hospital stays should be aware of this, and use joins with time as necessary.

Table columns

Name	Postgres data type	Example value
microevent_id	INTEGER NOT NULL	1234567
subject_id	INTEGER NOT NULL	12078372
hadm_id	INTEGER	29450599
micro_specimen_id	INTEGER NOT NULL	6386644
order_provider_id	VARCHAR(10)	P12ABC
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.

micro_specimen_id

Uniquely denoted the specimen from which the microbiology measurement was made. Most microbiology measurements are made on patient derived samples (specimens) such as blood, urine, and so on. Often multiple measurements are made on the same sample. The micro_specimen_id will group measurements made on the same sample, e.g. organisms which grew from the same blood sample.

order_provider_id

order_provider_id provides an anonymous identifier for the provider who ordered the microbiology test. Provider identifiers follow a consistent pattern: the letter “P”, followed by either three numbers, followed by two letters or two numbers. For example, “P003AB”, “P00102”, “P1248B”, etc. Provider identifiers are randomly generated and do not have any inherent meaning aside from uniquely identifying the same provider across the database.

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.