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Guide to the Application of Genotyping to Tuberculosis Prevention and Control										Related Pages
										**Introduction to Tuberculosis Genotyping**
**Overview of the CDC Tuberculosis Genotyping Program**
Two genotyping laboratories, one in Michigan and one in California, are under contract with CDC to provide genotyping services to TB programs in the United States. TB programs that have been approved to participate in the CDC Tuberculosis Genotyping Program may submit to a genotyping laboratory one isolate from each culture-positive patient with TB within their jurisdictions. In rare circumstances, TB programs may submit additional isolates from the same patient. These circumstances are described in Chapter 5, *Developing a TB Genotyping Program*. The genotyping laboratories will analyze isolates from current patients, but TB programs may request permission to submit selected isolates collected in the past. Although the implementation of universal genotyping (i.e., submitting one isolate from every culture-positive patient with TB) has substantial benefits, a TB program does not have to submit a particular number or percentage of isolates to participate in the program.
The genotyping laboratories will use three genotyping methods: **spoligotyping**, mycobacterial interspersed repetitive units (**MIRU**) analysis, and IS*6110*-based restriction fragment length polymorphism (**RFLP**) analysis. Spoligotyping and MIRU analysis are based on the polymerase chain reaction (**PCR**). Together, these methods will be referred to as PCR genotyping tests. The genotyping laboratories will analyze all the submitted isolates by both PCR genotyping tests. Under certain circumstances and upon the request of the TB program, isolates that have matching genotypes by both spoligotyping and MIRU analysis can be tested by RFLP analysis. The genotyping services are free to TB programs, and CDC pays shipping costs for isolates shipped to genotyping laboratories.
As of March, 2010, genotyping data are submitted, maintained, and accessed through CDC’s secure, online tuberculosis genotyping information system (TB GIMS).
							
					
						Page last reviewed:  September 1, 2012					Content source: 	Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention homeGuide to the Application of Genotyping to Tuberculosis Prevention and Control
Acknowledgments
Introduction to Tuberculosis Genotypingplus icon
Introduction to this Guide
Overview of Tuberculosis Genotyping
Overview of the CDC Tuberculosis Genotyping Program
TB Program Eligibility and Application Procedures
Tuberculosis Genotyping Case Studiesplus icon
Investigation of a Genotyping Cluster in a Low-Incidence State
Apparent Genotyping Cluster among Recent Immigrants from the Philippines
False-Positive Culture Investigation
Algorithm to Detect False-Positive Cultures
A Misdiagnosis that was Identified with Genotyping
Genotyping Used to Improve Contact and Cluster Investigations
Identification of Nontraditional Transmission Settings
Investigation of a Multistate Tuberculosis Outbreak
Homeless Shelter Outbreak Investigation
Using Genotyping to Evaluate the Impact of a Screening Program
CDC Tuberculosis Genotyping Laboratory Proceduresplus icon
Science behind Tuberculosis Genotyping
Description of Genotyping Methods
Submission of Isolates
Genotyping Results, Designation of Clusters, and Reporting
Suspected False-Positive Cultures
IS*6110*-based RFLP Analysis
Combining Genotyping and Epidemiologic Data to Improve Our Understanding of TB Transmissionplus icon
Definitions
Reading the Genotyping Laboratory Report
Comparing Genotyping and Epidemiologic Results from Two TB Patients
Comparing Genotyping and Epidemiologic Results from Three or More TB Patients
Clustering as a Surrogate Measure of Recent Transmission
Developing a Tuberculosis Genotyping Programplus icon
Developing a Written Plan
Initial Decisions
Establishing Procedures for:plus icon
Submitting Isolates
Receiving and Acting on Genotyping Results
Requesting RFLP Analysis
Submitting Additional Isolates from the Same Patient
Comparing Genotyping Results between Jurisdictions
False-Positive Cultures
Database Management and Quality Control
Special Issues
Applying Genotyping Results to Tuberculosis Control Practicesplus icon
Evaluating Matching Genotypes
Evaluating Nonmatching Genotypes
Suspected False-Positive Culture Investigations
Expanded Contact Investigations
Outbreak Investigations
Cluster Investigations
Monitoring Trends
Appendicesplus icon
Appendix A: Glossary and Abbreviations
Appendix B: References and Useful Resourcesplus icon
References Cited in the Guide
NTGSN Special Issue References
Information on Packaging and Shipping Infectious Substances
Core Steps of an Outbreak Investigation
Consultants Available to Offer Guidance To receive email updates about this page, enter your email address: Email Address			What's this?				Submit


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