Concept: Chlamydia - Method of Identification

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Concept Description

Last Updated: 2019-01-17

Introduction
    This concept provides a working definition of chlamydia and describes the methods used at MCHP to investigate chlamydia in the administrative data held in the Manitoba Population Research Data Repository. The concept lists the ICD-9-CM and ICD-10-CA diagnostic codes to identify chlamydia in the hospital abstracts data and the medical services data, and lists the codes that are used in laboratory tests to investigate its presence in the population. SAS code (internal access only) is also available for working with the laboratory data.
Definition
MCHP Chlamydia Algorithms
    The following two methods have been used at MCHP to determine testing and to identify individuals with chlamydia.
1. Brownell et al. (2012)
    In Brownell et al. (2012), the percent of youths aged 13 to 19 years with at least one positive detection for chlamydia in the Cadham Provincial Laboratory (CPL) database in the fiscal year 2008/09 was examined. A positive detection was defined as:

    • Chlamydia trachomatis identified in the Clinical Microbiology Section - Organism file (see Table 1 for the AUXCD5 code), OR

    • chlamydia detected or chlamydia positive in the Clinical Microbiology Section - Results file (see Table 2 for the AUXCD5 codes).

    NOTE: Table 3 lists the chlamydia tests available in the Serology Section of the CPL data. In Brownell et al. (2012), this was investigated and reviewed but not included as part of the chlamydia results.

    The percent of youths with at least one positive detection for chlamydia in Manitoba was more than three times higher for females (2.62%) than for males (0.83%) (p<0.0001) with a provincial average of 1.71%. The lowest frequency was in the Rural South (0.76%) and the highest was in the North (5.03%). A Socioeconomic Status (SES) gradient for chlamydia was identified with the highest percentage found in the rural and urban areas with the lowest income, and the percent decreases as area-level income increases. Furthermore, the lowest income quintiles had much higher positive chlamydia detections in both urban and rural areas. For more information read the section Chlamydia in Brownell et al. (2012).
Table 1 - Chlamydia: Clinical Microbiology Section - Organism
    STARTDT 1 STOPDT 2 AUXCD5 DESCR40
    4/10/1992 1/1/2099 CHLT CHLAMYDIA TRACHOMATIS

    1 - The date that the code was created in the file.
    2 - The date that the code became inactive.

Table 2 - Chlamydia: Clinical Microbiology Section - Results
    STARTDT 1 STOPDT 2 AUXCD5 DESCR70
    4/10/1992 1/1/2099 CHD CHLAMYDIA DETECTED
    4/15/1999 1/1/2099 CHLPN CHLAMYDIA PNEUMONIAE NEGATIVE
    5/27/1999 1/1/2099 CHLPP CHLAMYDIA PNEUMONIAE POSITIVE
    4/10/1992 1/1/2099 CHNCT CHLAMYDIA SPECIES DETECTED; NOT C. TRACHOMATIS
    4/10/1992 1/1/2099 CHND CHLAMYDIA NEGATIVE
    4/10/1992 4/10/1992 CHP CHLAMYDIA POSITIVE
    4/10/1992 1/1/2099 CHPND CHLAMYDIA PSITTACI NOT DETECTED
    6/22/2000 1/1/2099 CPN CHLAMYDIA PSITTACI PCR NEGATIVE
    5/14/2002 1/1/2099 CTPN CHLAMYDIA TRACHOMATIS PCR NEGATIVE
    2/16/1996 1/1/2099 LCRRD LCDC RESEARCH RESULT: CHLAMYDIA DETECTED
    2/16/1996 1/1/2099 LCRRN LCDC RESEARCH RESULTS: CHLAMYDIA NOT DETECTED

    1 - The date that the code was created in the file.
    2 - The date that the code became inactive.

Table 3 - Chlamydia: Serology Section
    STARTDT 1 STOPDT 2 AUXCD5 DESCR40
    1/1/1990 1/1/2099 CHDCF CHLAMYDIA SPP CF
    1/1/1990 1/1/2099 CHDM CHLAMYDIA SPP IGM
    11/4/1994 1/1/2099 CPNUG CHLAMYDIA PNEUMONIAE IGG
    11/4/1994 1/1/2099 CPNUM CHLAMYDIA PNEUMONIAE IGM
    11/4/1994 1/1/2099 CPSTG CHLAMYDIA PSITTACI IGG
    11/4/1994 1/1/2099 CPSTM CHLAMYDIA PSITTACI IGM
    11/4/1994 1/1/2099 CTRAG CHLAMYDIA TRACHOMATIS IGG
    11/4/1994 1/1/2099 CTRAM CHLAMYDIA TRACHOMATIS IGM

    1 - The date that the code was created in the file.
    2 - The date that the code became inactive.
2. Lix et al. (2012)
    In Lix et al. (2012), the Cadham Provincial Laboratory (CPL) database from 1992/93 to 2008/09 was used to identify the total number of chlamydia tests and the frequency of positive tests (laboratory-confirmed cases) by fiscal year in Manitoba. Approximately 5% of all chlamydia tests were positive in each of the study years.

    Data from the CPL Clinical Microbiology Section - Organism file was used to identify the pathogenic bacterium Chlamydia trachomatis. Table 1 above reports the code for this organism. The Clinical Microbiology Section - Results file was used to identify the CPL number of chlamydia tests and the frequency of positive laboratory-confirmed cases in Manitoba. Table 2 lists the codes used to report the results of these tests. For more information on CPL, see the CADHAM Provincial Laboratory (CPL) - Overview of Services and Data concept.
Comparison of Lab Data to Hospital Discharge Abstracts and Medical Services Data
SAS Code
    SAS code for identifying chlamydia tests in the Cadham Provincial Laboratory is available in the SAS code and formats section below (internal access only).
Limitations / Cautions
  • Cadham Provincial Laboratory (CPL) performs virtually all tests for chlamydia in Manitoba, but laboratory data may not capture all cases in a jurisdiction.

  • The technology for testing various STI or STBBIs has changed over the last several years; therefore examining trends in these infections may not reflect actual trends in the infections themselves but changes in detection. For this reason, chlamydia was examined not over time but for a single fiscal year (2008/09) in Brownell et al. (2012) .

  • Over time, the diagnosis recorded In the Medical Services / Physician Claims data is limited to one, 3-digit ICD-9-CM code. In some cases, the 3-digit code is not specific enough to uniquely identify conditions and if used, may over report certain conditions. In December 2018, a 5-digit diagnosis code variable was added to the Medical Services data. If recorded, the first 3-digits of both the 3-digit and 5-digit diagnosis code variables will match exactly. The 5-digit diagnosis code variable applies to records from 2015/16 forward.

  • A value of P [Positive] to identify a positive test result in the POSNEG field [Positive-Negative] or the presence of specific AUXCD5 codes for chlamydia detection in the CPL data was used to determine if an individual was positive for chlamydia.

  • The AUXCD5 codes used to identify chlamydia in the CPL data should be verified at the beginning of each new study to ensure they are up-to-date.

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References 

  • Brownell M, Chartier M, Santos R, Ekuma O, Au W, Sarkar J, MacWilliam L, Burland E, Koseva I, Guenette W. How are Manitoba's Children Doing? Winnipeg, MB: Manitoba Centre for Health Policy, 2012. [Summary] [Full Report] [Data extras] [Errata] (View)
  • Dickerson MB, Johnston J, Delea TE, White A, Andrews E. The casual role for genital ulcer disease as a risk factor for transmission of human-immunodeficiency virus: An application of the Bradford Hill Criteria. Sexually Transmitted Diseases 1996;23(5):429-440.(View)
  • Lix L, Smith M, Azimaee M, Dahl M, Nicol P, Burchill C, Burland E, Goh C, Schultz J, Bailly A. A Systematic Investigation of Manitoba's Provincial Laboratory Data. Winnipeg, MB: Manitoba Centre for Health Policy, 2012. [Summary] [Full Report] (View)