Guide to the Application of Genotyping to Tuberculosis Prevention and Control

Introduction to Tuberculosis Genotyping

Introduction to this Guide

This guide provides an introduction to the application of tuberculosis (TB) genotyping to TB control practices and to the Centers for Disease Control and Prevention (CDC) TB Genotyping Program. It was written by the National Tuberculosis Controllers Association (NTCA)/CDC Advisory Group on Tuberculosis Genotyping and is intended for TB controllers, epidemiologists, laboratorians, and other program staff members who will be involved in submitting isolates for genotyping, analyzing and responding to genotyping results, or using genotyping data to monitor TB transmission trends.

This guide does not contain specific directions on how a TB control program must carry out its genotyping program. The CDC genotyping program is not a research effort, and participating state and local programs are not required to carry out a protocol, submit a certain number of isolates, or collect specific data. Rather, this guide provides general guidance about how to utilize the genotyping laboratories, how to understand genotyping results, and how to apply those results to improve TB control practices. For those interested in the specific procedures used by other TB genotyping programs, the Maryland TB program and the New York City TB program have agreed to share their procedure manuals; those documents can be downloaded from our TB genotyping WebBoard at

Understanding TB genotyping results is not difficult, but it involves learning a new vocabulary. It also involves establishing new procedures to ensure that the genotyping results can easily be combined with appropriate epidemiologic data to identify instances of recent TB transmission. This new vocabulary and these new procedures are the focus of this guide. Hopefully, we have developed a guide that helps you master this new subject.

In the following paragraphs, key concepts are introduced. These concepts are developed further in the relevant chapters of the guide. Finally, a glossary in Appendix A defines important concepts. Throughout the guide, tables, figures, and text boxes sum up important points made in the text. An electronic copy of this guide, the Isolate Submission Form, and other genotyping documents can be downloaded from the CDC Tuberculosis Genotyping Program’s WebBoard at Copies of the guide can be ordered by sending an e-mail to