Guide to the Application of Genotyping to Tuberculosis Prevention and Control Handbook for TB Controllers, Epidemiologists, Laboratorians, and Other Program Staff Prepared by the National Tuberculosis Controllers Association / Centers for Disease Control and Prevention Advisory Group on Tuberculosis Genotyping June 2004 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 http://web-tb.forum.cdc.gov Copies of the guide can be ordered by sending an e-mail to Dr. Patrick Moonan at [email protected]. Suggested citation: National TB Controllers Association / CDC Advisory Group on Tuberculosis Genotyping. Guide to the Application of Genotyping to Tuberculosis Prevention and Control. Atlanta, GA: US Department of Health and Human Services, CDC; June 2004. TM Contents Acknowledgments ...........................................................................................................iii 1. Introduction to Tuberculosis Genotyping ...............................................................1 Introduction to this Guide Overview of Tuberculosis Genotyping Overview of the CDC Tuberculosis Genotyping Program TB Program Eligibility and Application Procedures 2. Tuberculosis Genotyping Case Studies ..................................................................5 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 3. CDC Tuberculosis Genotyping Laboratory Procedures ......................................15 Science behind Tuberculosis Genotyping Description of Genotyping Methods Submission of Isolates Genotyping Results, Designation of Clusters, and Reporting Suspected False-Positive Cultures IS6110-based RFLP Analysis 4. Combining Genotyping and Epidemiologic Data to Improve Our Understanding of Tuberculosis Transmission ................................................25 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 5. Developing a Tuberculosis Genotyping Program .................................................35 Developing a Written Plan Initial Decisions Establishing Procedures for: • 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 i 6. Applying Genotyping Results to Tuberculosis Control Practices ......................49 Evaluating Matching Genotypes Evaluating Nonmatching Genotypes Suspected False-Positive Culture Investigations Expanded Contact Investigations Outbreak Investigations Cluster Investigations Monitoring Trends 7. Appendices ...............................................................................................................63 Appendix A: Glossary and Abbreviations Appendix B: References and Useful Resources ii Acknowledgments The contents of this guide represent the dedication and hard work of our TB control community. Numerous people, despite having limited resources and working overtime on numerous competing projects, have contributed to the multiple tasks involved in bringing material of this complexity together into what we hope is a coherent whole. The editors gratefully acknowledge each contributor. We also acknowledge and thank Angie Weaver and Rachel Wilson for their excellent editorial contributions to the guide. Editors Thomas Navin, MD National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Lisa Rosenblum, MD, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Charles Wallace, PhD TB Elimination Division Texas Department of Health Austin, TX Sue Etkind, RN, MS TB Control and Prevention Massachusetts Department of Health and Human Service Jamaica Plain, MA iii Writing Group Members Jack Crawford, PhD Scott McNabb, PhD, MS National Center for HIV, STD, and TB Prevention National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Centers for Disease Control and Prevention Atlanta, GA Atlanta, GA Wendy Cronin, PhD Tanya Oemig, NRM Maryland State Department of Health and Mental Wisconsin Department of Health and Family Hygiene Services Baltimore, MD Madison, WI Jeff Driscoll, PhD Margaret Oxtoby, MD, MPH Wadsworth Center Bureau of TB Control New York State Department of Health New York State Department of Health Albany, NY Albany, NY Cynthia Driver, RN, MPH Walter Page Epidemiology Office National Tuberculosis Controllers Association Bureau of TB Control Atlanta, GA New York City Department of Health New York, NY Jennifer Flood, MD California Department of Health Services Berkeley, CA Reuben Granich, MD, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Kashef Ijaz, MD, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Steve Kammerer National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Peter McElroy, PhD, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA iv Working Group Members Tracy Agerton, RN, MPH Barry Kreiswirth, PhD TB Control Program Public Health Research Institute New York City Department of Health Newark, NJ New York, NY Mark Lobato, MD Peter Barnes, MD National Center for HIV, STD, and TB Prevention Center for Pulmonary and Infectious Disease Control Centers for Disease Control and Prevention Departments of Medicine, Cell Biology, and Atlanta, GA Immunology University of Texas Health Center Bereneice M. Madison, PhD Tyler, TX National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Carol Berglund Atlanta, GA National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Beverly Metchock, DrPH Atlanta, GA National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Chris Braden, MD Atlanta, GA National Center for Infectious Diseases Centers for Disease Control and Prevention DeNay Porter-Kirkpatrick, MSN Atlanta, GA The University of Alabama at Birmingham Birmingham, AL Bill Burman, MD Denver Public Health and Hospitals Authority Sandy Price Denver, CO National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Don Cave, PhD Atlanta, GA University of Arkansas for Medical Sciences Little Rock, AR Sharon Sharnprapai, MS State Laboratory Institute Jeanne Courval, PhD Jamaica Plain, MA National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Sumi Sun, MPH Atlanta, GA California Department of Health Berkeley, CA Don Cunningham, BS Division of Tuberculosis Zachary Taylor, MD, MPH Arkansas Department of Health National Center for HIV, STD, and TB Prevention Little Rock, AR Centers for Disease Control and Prevention Atlanta, GA Ed Desmond, PhD California Department of Health Wanda Walton, MEd, PhD Berkeley, CA National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Loretta H. Gossett, RN, MA Atlanta, GA Anne Arundel County Department of Health Annapolis, MD Nancy G. Warren, PhD Bureau of Laboratories Nancy Hooper, BA Pennsylvania Department of Health Maryland Department of Health and Mental Hygiene Lionville, PA Baltimore, MD Rosemary Humes, MS, MT (ASCP), SM Liaison to Association of Public Health Laboratories Washington, DC v Technical Consultants Gabrielle Benenson, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Melanie Davis, MS National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Hsin-Hsin Foo, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA Michele Huitric, MPH National Center for HIV, STD, and TB Prevention Centers for Disease Control and Prevention Atlanta, GA vi Introduction to Tuberculosis Genotyping 1 Introduction to Tuberculosis Genotyping Chapter Preview 1. Introduction to this Guide 2. Overview of Tuberculosis Genotyping 3. Overview of the CDC Tuberculosis Genotyping Program 4. TB Program Eligibility and Application Procedures 1. 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