Concept: CADHAM Provincial Laboratory (CPL) - Overview of Services and Data

Introduction

This concept provides information about the CADHAM Provincial Laboratory (CPL), based on a presentation by Matt Dahl at the August 22, 2012 Data Analyst meeting and the deliverable A Systematic Investigation of Manitoba's Provincial Laboratory Data (subsequently referred to as the CADHAM Lab deliverable in this concept). This deliverable, released on December 3, 2012, focuses on the CPL data and the MCHP Data Quality Framework.

The information in this concept includes an overview of services provided by CPL, the CPL data available on the SPD Server, a starting point for using the data, examples of use and a list of measures from the CADHAM Lab deliverable, and finally cautions when using the data. Links are provided to the on-line MCHP Glossary for related terms from this deliverable.

Overview of CPL Services

The CADHAM Provincial Laboratory (CPL) is Manitoba's provincial public health laboratory. It provides the following services:


• early detection of health risks associated with infectious agents;
  
• monitoring of outbreak investigations; and
  
• identification of causes of disease to help in treatment and prevention

These services are divided into four distinct sections:


• Clinical Microbiology
  
  • investigation of human bacterial enteric pathogens and food borne illness (e.g. salmonella);
    
  • sexually transmitted infections (STIs) (e.g. chlamydia, gonorrhea);
    
  • detection, isolation and characterization of organisms or toxins from clinical specimens
  
  
• Virology/Virus Detection
  
  • monitors viral isolates to ensure vaccine-preventable diseases are not spreading;
    
  • isolation, detection, and identification of human viral pathogens
  
  
• Parasitology and Serology
  
  • provide surveillance and diagnosis for public health programs (e.g. prenatal screening for syphilis, hepatitis B, and rubella);
    
  • detection and determination of an antigen or antibody
    
  • detect acute and chronic infections due to viral, bacterial, fungal or parasitic agents
    
  • immune status assessment
  
  
• Newborn Screening and Public Health Chemistry
  
  ( NOTE: this service data is not currently available in MCHP Data Repository).

Data Available on SPD Server

The Cadham Provincial Laboratory (CPL) Data Description is available on-line in the MCHP Data Repository. Currently, the data available covers the fiscal years 1992/93 to July 2010, although 2009/10 is not complete - there is a drop off near the end of the fiscal year (approximately the last 3 months). All files are in the "HEALTH" directory on the SPD server and all files begin with the "MHCPL_" prefix. The files include:


• Virology/Virus Detection Section - Requisitions file, Tests file;
  
• Serology/Parasitology Section - Requisitions file, Serology Tests file, Parasitology Tests file;
  
• Clinical Microbiology Section - Requisitions file, Results file, Organisms file;
  
• Provider/Physician file;
  
• Referring Facility file; and
  
• 18 Auxiliary files that provide interpretation of codes contained in the above files.

A Starting Point for Using the Data - Variables and SAS Code

On all requisitions data there is a variable that indicates the number of tests requested for that section (nserology, nparasitology, nvirsusdetection, ncmresults, ncmorganisms). There will be that number of records on the corresponding tests/results/organisms dataset for that requisition. Some of the most important variables in this data include:


• SCRPHIN - MCHP scrambled PHIN
  
• Requisitionnumber - requisition number
  
• Receiveddt - date specimen was received at lab
  
• Specimentdt - date the specimen was taken
  
• Specimensource - code for the specimen source
  
• Posneg - positive (P) or negative (N) test result
  
• Result (serology) - code for serology/parasitology result
  
• Serologytest - code for serology test done
  
• Parasitologytest - code for parasitology test done
  
• Parasitologyparasite1 - 5 - code for parasite found due to the testing
  
• Parasitologyresult1 - 5 - code for parasitology test result (up to 5 results)
  
• Virus - code for viral result of the testing
  
• Result (virus detection) - code for virus detection result
  
• Results1 - 6 - code for clinical microbiology results (up to 6 results)
  
• Organism - code for clinical microbiology organism identified in the findings of the testing

The following SAS code examples match the tests/results records with the appropriate requisitions for each different section of the CPL. The SAS program examples that are available include:


• clinical_microbiology_organisms_section.sas.txt
  
• clinical_microbiology_results_section.sas.txt
  
• parasitology_section.sas.txt
  
• serology_section.sas.txt
  
• virus_detection_section.sas.txt
  
  NOTE: The SAS programs listed above are available in the SAS Code and Formats section below (internal access only).

Examples of Use

In the CADHAM Lab deliverable, both Sexually Transmitted Infections (STIs) and Tuberculosis (TB) were investigated:


• Sexually Transmitted Infections (STIs) :
  
  • Gonorrhea (clinical microbiology section)
    
    • identify tests by the results and based on the result(s) provided determine whether or not it is a positive or negative result.
      
    • additional tests identified by the gonorrhea organism (NG) found.
    
    
  • Chlamydia (serology and clinical microbiology section)
    
    • identify tests by the results and based on the result(s) provided determine whether or not it is a positive or negative result.
      
    • additional tests identified by the chlamydia organism (CHLT) found.
      
    • additional tests identified in the serology section based on the serologytest variable. Use the posneg variable to determine whether or not it is a positive or negative result.
    
    
  • Syphilis (serology section)
    
    • identify tests by the serologytest variable. Use the posneg variable to determine whether or not it is a positive or negative result.
    
    
  • Human Immunodeficiency Virus (HIV) (serology section)
    
    • identify tests by the serologytest variable. Use the posneg variable to determine whether or not it is a positive or negative result.
      
    • Note: The majority of HIV tests are anonymous and do not have a linkable scrphin. Only the most recent year or two has HIV tests with linkable scrphin.
  
  
• Tuberculosis (clinical microbiology organisms section)
  
  • identify tests by the tuberculosis organism codes.

List of Measures from the CADHAM Lab Deliverable

The measures / indicators from the CADHAM Lab deliverable include:


• number of requisitions overall and by section
  
• number of tests overall and by section
  
• percent of population with at least one test
  
• percent of prenatal population with at least one test
  
• percent of prenatal population with at least one rubella, syphilis, HIV, hep B, or hep C test
  
• tests by referring provider type
  
• tests by referring facility type
  
• number of positive/negative chlamydia, gonorrhea, and syphilis tests

Cautions

The following cautions should be considered when working with the CADHAM Lab data:


• A requisition appears to be able to cross multiple sections with high consistency except with the serology section. i.e. If the same requisition number appears in multiple sections then it is one requisition (same patient, received date, specimen date, CPL patient number, etc.) (serology needs to be looked at more closely as patient information from other sections do not match up at or near 100% for the same requisition number)
  
  
• Some tests are not consistently done over time. How outbreaks are handled is unsure. Testing may be done until there can be an official outbreak considered, and then testing may slow down or stop (H1N1?).
  
  
• Some tests may have been done at CADHAM, but are no longer done there, so there will be a sudden drop off in tests if that is the case (i.e.: Tuberculosis (TB)).