Guide to the Application of Genotyping to Tuberculosis Prevention and Control
Developing a Tuberculosis Genotyping Program
An important use of genotyping is to detect or confirm suspected false-positive cultures that are due to cross contamination, mislabeled specimens, and other errors. Procedures for dealing with false-positive cultures differ somewhat, depending on whether the error was suspected before the genotyping results were known or the error was identified as a result of the genotyping laboratory report.
“Genotyping of TB isolates is particularly useful in the evaluation of patients who have only a single culture-positive specimen, a population for whom up to 40% of the isolates are false-positive. Timely evaluation of these isolates prevents unwarranted isolation, treatment and contact investigations. Genotyping is also useful over the intermediate time period of months to several years in clarifying the role of recent transmission in high-risk populations and methods of intervention. Genotyping in Denver identified a large outbreak that was introduced by a patient who defaulted from TB treatment in Louisiana. This data lead to an ongoing TB screening program that has detected such cases earlier and lead us to aggressively pursue the location of defaulters who leave our area.”
Suspected False-Positive Cultures
A laboratory may suspect that an M. tuberculosis-positive culture represents an error when two or more specimens processed on the same day become positive or when only one culture out of many from the same patient becomes positive. A clinician may suspect a false-positive culture when TB is diagnosed for a patient on the basis of a single culture but the patient has an incompatible clinical picture.
When a false-positive culture is suspected, the laboratory or clinician may want to verify this suspicion before they report the patient as having a new case. The TB Genotyping Isolate Submission Form includes a field to identify an isolate as a possible false-positive culture (the column title is “suspected_false_positive”). When the suspicion of a false-positive culture is flagged on the form, the genotyping laboratory will send the genotyping results to the submitting laboratory and to the TB program. The TB program should discuss this procedure with laboratories in its jurisdiction and agree on a process for submission of the isolates, either directly or through the state laboratory, and perhaps use an expedited protocol. All isolates submitted to the genotyping laboratory will receive rapid turnaround, so there is no need to request expedited typing. When the spoligotype and MIRU type for a suspected false-positive culture match the genotype of the putative source isolate, this provides strong evidence that the culture is false-positive. In this case, there is no need for confirmation by IS6110-based RFLP analysis.
Unsuspected False-Positive Cultures
False-positive cultures can also be detected by analysis of genotyping results. A TB program’s genotyping plan should include a procedure for evaluating all matching isolates for the possibility that one or more represent an unsuspected false-positive culture. Unsuspected false-positive culture results that are identified on the basis of matching PCR genotyping results should be confirmed with RFLP analysis. The genotyping laboratories will not have sufficient patient or laboratory information to help decide whether particular matching isolates represent false-positive cultures, except in the instance of contamination with common laboratory control strains.