Microbiology Labs
The Microbiology Labs module contains additional specimen, organism, and antibiotic susceptibility data that does not fit into the Labs File.
Target Date
This module has two options for its target date definition. Note that only one option may be chosen per instance.
1. (Recommended) For a given target date, extract all microbiology labs taken on that date.
2. For a given target date, determine the list of all cases for that date. Then, extract all labs for those patients that were taken within the date range of 365 days
before and after anesthesia start.
File Columns: Base lab component
Column Name
Nullable?
Data Type
Description
Micro_Lab_ID
No
varchar
The identifier of the lab component result.
Patient_ID
No
varchar
The patient identifier, must be the same identifier given in the "Patients" file
Encounter_ID
Yes
varchar
The encounter / admission / visit identifier
Order_ID
No
varchar
The row identifier of the parent lab order
Order_Procedure_Type_ID
No
varchar
The variable identifier of the lab procedure
Order_Procedure_Type_Name
No
varchar
The variable name of the of the lab procedure
Lab_Component_Type_ID
No
varchar
The identifier of the child component of the lab procedure
Lab_Component_Type_Name
No
varchar
The name of the child component of the lab procedure (lab detail)
Specimen_Type_ID
No
varchar
The variable identifier of the specimen type
Specimen_Type_Name
No
varchar
The variable name of the specimen type
Order_Result
No
varchar
The value of the lab result. Those with multiple lines/results should be appended together.
Order_Result_Comments
Yes
varchar
Additional details/comments regarding the lab result, such as describing exceptional circumstances
Order_Result_Status
Yes
varchar
Describes the status of the lab result
Collection_Time
Yes
datetime
The time the lab sample was obtained
Result_Time
No
datetime
The time the lab result was returned
Additional Column Details
Micro_Lab_ID
It may be necessary to manufacture this row identifier if one does not exist in the source system. One recommended approach is to concatenate other identifiers:
PatientId-OrderId-ComponentId-Line. When doing so, be aware of the character limit for this column.
Specimen_Type_ID
If one doesn't exist, reuse the value for Speciment_Type_Name
Rarely, some lab values will have an additional codified representation from a standard lexicon. For example, a value indicating a diagnosis of “diabetes” may also have a
value code of “E11.9”, the ICD-10 representation of diabetes. The vast majority of lab results do not have such a code and therefore this field is commonly blank.
Encounter_ID
Optional but strongly recommended.
File Columns: Antibiotic Sensitivity Findings
Column Name
Nullable?
Data Type
Description
Isolate_Sub_ID
Yes*
integer
The row identifier of the specific isolate used on the order component.
Isolate_Organism_ID
Yes*
varchar
The organism isolated in the lab component
Isolate_Organism_Name
Yes*
varchar
The organism isolated in the lab component
Sensitivity_Agent_ID
Yes*
varchar
The antibiotic the isolate organism was tested on
Sensitivity_Agent_Name
Yes*
varchar
The antibiotic the isolate organism was tested on
Sensitivity_Value
Yes**
varchar
The lowest concentration of antibiotic required to inhibit growth of the isolate_organism
Sensitivity_Value_Units
Yes**
varchar
The units of measure used in the Sensitivity_Value field
Sensitivity_Interpretation
Yes**
varchar
The sensitivity value interpretation
Sensitivity_Final_Status
Yes**
varchar
The status of the sensitivity findings
Additional Column Details
Isolate_Sub_ID
Useful for grouping different isolates on either the same organism or different organisms.
Specimen_Type_ID
If one doesn't exist, reuse the value for Speciment_Type_Name
Encounter_ID
Optional but strongly recommended.
