Concept: Chlamydia - Method of Identification

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

Chlamydia is a sexually transmitted infection (STI) caused by the bacterium Chlamydia trachomatis. Untreated infection may lead to epididymitis in men or pelvic inflammatory disease, tubal infertility, and ectopic pregnancy in women ( Public Health Agency of Canada Website - Chlamydia). It may also increase the risk of contacting Human Immunodeficiency Virus (HIV) if left untreated (Dickerson et al., 1996).

Many individuals infected with chlamydia are asymptomatic, thus providing a silent spread of the STI ( Public Health Agency of Canada Website - Chlamydia ). Because of the significant public health implications, chlamydia is a notifiable disease in Canada since 1990 ( Lix et al., 2012). All positive laboratory cases of chlamydia are reportable to the Communicable Disease Control Branch of Manitoba Health and Healthy Living. For more information on chlamydia, see the Public Health Agency of Canada Website - Chlamydia.

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

Chlamydia diagnoses from the hospital abstracts data and the medical services data were compared to the CPL data. ICD-9-CM codes 079, V02, V02.8, V73, V73.88, V73.98 and ICD-10-CA codes A54, A56, A70 were used to identify chlamydia. Only a small proportion of positive tests (laboratory-confirmed cases) for chlamydia had a corresponding diagnosis in hospital or physician claims data, regardless of the size of the reference window applied to the data (diagnosis within 30, 90, and 180 days before or after the index date in the CPL data). For more information on how chlamydia was investigated in the CPL data, read the section titled Case Study #3: Sexually Transmitted Infection Tests in CPL Data and Sexually Transmitted Infection Diagnoses in Hospital and Physician Billing Records in Lix et al. (2012).

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.