Guide to the Application of Genotyping to Tuberculosis Prevention and Control
Developing a Tuberculosis Genotyping Program
Database Management and Quality Control
Genotyping programs rely on the collection and analysis of large quantities of data. TB programs that are implementing genotyping programs for the first time have to address database management issues. Although a detailed discussion of the options for database management is beyond the scope of this document, this section summarizes key points.
Central databases for isolate tracking, laboratory results, and epidemiologic data are essential. Because cluster investigations are an epidemiologic activity, the TB program should maintain the principal databases for isolates and contact investigations. Although clustering occurs most frequently in relatively small geographic areas (i.e., a single county or adjacent counties), genotyping clusters can be widespread and are not bound by state lines. Including the number for the Report of a Verified Case of Tuberculosis (RVCT) or the state case number in all database entries will allow a comparison of data from different jurisdictions.
In order for field workers to have access to needed information, data must be abstracted from different databases and merged. The information in these databases can enable TB programs to identify easily patients with matching genotypes and epidemiologic links.
The TB program should establish a database management system that includes and links at least three elements.
- TB surveillance data (e.g., data collected for the RVCT). TB surveillance data contain demographic information, patient’s risk factors, and sputum and smear results.
- Laboratory results data. At a minimum, data will include a) the patient’s name, b) RVCT or state case number, c) patient’s status (e.g., isolate represents a verified case of TB, a false-positive culture, or a duplicate isolate), d) patient’s county of residence, e) accession numbers of submitting and genotyping laboratories, f) names of originating and submitting laboratories, g) specimen source, h) dates of specimen collection and culture report, i) drug-susceptibility pattern, j) genotyping laboratory report results, and k) cluster designations. Because a suspicion of a false-positive culture is often based on the presence of only a single positive culture, this information should be captured in the database as well.
- Epidemiologic data. A database is essential for maintaining information about relationships between and among every patient with matching genotypes so that results can be analyzed effectively. At a minimum, the database should include a) the patient’s name; b) RVCT or state case number; c) case report date; d) whether patient has epidemiologic links with other clustered patients; e) source patient’s name; f) setting of transmission; and g) whether the link was established by a contact investigation, a cluster investigation, or another method.
Collecting data on certain process measures is essential to ensure and improve the quality of the genotyping program. For example, turnaround times should be monitored so that progress in reducing turnaround can be documented. TB programs should decide what process measures they will collect and evaluate. Programs should consider collecting data to provide answers to the following questions:
- Of the isolates that met submission criteria, how many were submitted or lost or are pending?
- How much time elapsed between the date of culture report and the date of isolate submission?
- How much time elapsed between the date of isolate submission and the date the TB program received the genotyping laboratory results?
Epidemiologic investigation process measures are equally important and should include the following questions:
- How much time elapsed between the identification of a cluster that required a cluster investigation and a record review or patient interview?
- How many patient interviews were needed and how many were conducted?
- Why were needed interviews not conducted (e.g., patient lost, died, moved, or refused)?
- How many attempts were made to contact a patient (i.e., times and type of attempts)?
- How many epidemiologic links were identified and when (i.e., before or after genotyping results)?
Standard Forms for Data Collection
Standardized forms are required to ensure that data are collected in the same way for every patient. A template for collecting cluster investigation information in a standardized manner is posted on the WebBoard.
The form can be employed for cluster investigations in its present format, or it can be modified to suit the specific needs of a TB program.