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Guide to the Application of Genotyping to Tuberculosis Prevention and Control										Related Pages
										**Tuberculosis Genotyping Case Studies: How TB Programs Have Used Genotyping**
In this chapter, we will provide examples of how TB programs have used genotyping to assist them in conducting important TB control activities. Specifically, this chapter provides examples of how genotyping results have helped identify new, previously unrecognized transmission links between patients with TB, how they have been used effectively during outbreak investigations, and how these results can be used in the future to detect outbreaks at early stages. We will also describe how genotyping has been used to monitor epidemiologic trends, evaluate program performance, and identify instances of false-positive cultures that can result from mislabeling clinical specimens, cross-contamination of cultures, or other problems.
In the past, most programs have submitted only selected *M. tuberculosis* isolates for genotyping. Although selective genotyping provides new insights into TB transmission, the power of genotyping is increased considerably when isolates from all patients with culture-positive TB are genotyped, even before contact investigations or outbreak investigations raise the suspicion that there might be a link between patients. In reading the case studies that follow, pay attention to what advantages accrue to programs that institute selective genotyping and what advantages accrue only to programs that institute universal genotyping.
Most of the data that has been gathered about the utility of TB genotyping is based on the genotyping approach used by the TB programs that participated in the National Tuberculosis Genotyping and Surveillance Network (NTGSN) (Castro 2002). A special issue of the journal *Emerging Infectious Diseases* was devoted to presenting the findings of the NTGSN study and is available at http://wwwnc.cdc.gov/eid/articles/issue/8/11/table-of-contents.
The NTGSN study was based on IS*6110*-based RFLP analysis supplemented by spoligotyping for certain isolates. Data are still limited about how this past approach will compare with the current approach used by the CDC Tuberculosis Genotyping Program, which is based on spoligotyping and MIRU analysis of all isolates, with IS*6110*-based RFLP for only selected isolates (see Chapter 5, *Developing a Tuberculosis Genotyping Program**,*** for details about when RFLP is helpful). The first three of the following examples were reported by TB programs that are using the current approach; the others come from the National Tuberculosis Genotyping and Surveillance Network.
							
					
						Page last reviewed:  December 12, 2014					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
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