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Guide to the Application of Genotyping to Tuberculosis Prevention and Control										Related Pages
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**Appendix A: Glossary and Abbreviations**
**AFB**
Acid-fast bacilli. Microorganisms that retain certain applied stains after being rinsed with an acid solution. Most acid-fast organisms detected in patient specimens are mycobacteria. When viewed under the microscope using the Zhiel-Neelson staining method, *M. tuberculosis* bacteria appear red on a blue background. When AFB are seen on a stained smear of sputum or other specimen, a diagnosis of TB disease should be suspected, and the concentration of organisms per unit area of slide (the smear grade) correlates with the degree of infectiousness. The diagnosis of TB disease is usually not confirmed until a culture is grown and *M. tuberculosis* is identified. A positive nucleic acid amplification (NAA) test is useful as a confirmatory test.**Agarose gel electrophoresis**
A laboratory method used to separate molecules. IS*6110*-based RFLP uses agarose gel electrophoresis to separate DNA fragments by size.**BCG**
Bacille Calmette Gurin. A BCG isolate is commonly used as a control strain in spoligotyping assays.**Beijing strain**
An isolate of the Beijing strain of *M. tuberculosis* is commonly used as a control strain in spoligotyping assays, since it has an unusual octal designation: 00000000000371.**Casual contact**
Contact between a source case and someone else that is not prolonged and often that occurs in a nontraditional setting. The common teaching that TB is not transmitted by casual contact needs to be revised in light of genotyping studies that show it occurs more commonly than was once thought.**Chain of recent transmission**
Patients with TB who have transmitted *M. tuberculosis* among themselves recently. Genotyping provides additional information to traditional epidemiologic links to define chains of recent transmission, since patients who are involved in the same chain of recent transmission will almost always have *M. tuberculosis* isolates that have matching genotypes.**CLIA**
Clinical Laboratory Improvement Amendments. The CLIA program is operated by the Department of Health and Human Services to ensure quality laboratory testing.**Close contact**
A person who has shared the same air space with a person who has infectious TB disease and is among those of highest priority of triaged contacts based on historical, social, and epidemiologic data to warrant investigation.**Cluster**
A genotyping cluster is two or more *M. tuberculosis* isolates that share matching genotypes. An epidemiologic cluster is two or more persons with TB who share known epidemiologic links. See *Cluster investigation, Epidemiologic cluster, Genotyping cluster, epidemiologically confirmed genotyping cluster.***Cluster investigation**
An investigation to identify epidemiologic links between TB patients whose isolates have matching genotypes. A cluster investigation may consist of reviewing information from medical records and interviewing case managers and outreach workers. It can also involve interviewing TB patients. The term has also been used to describe an investigation of TB patients who share epidemiologic links before genotyping results are known.**Contact investigation**
An investigation of persons who have come into contact with a patient with infectious TB. The goals of a contact investigation are to identify additional persons with active TB, to determine if transmission occurred between the TB patient and the contacts, and to identify person with latent TB infection who are candidates for treatment.**Cross-jurisdiction transmission**
Transmission of TB from a patient who resides in one TB program jurisdiction to a person who lives in another TB program jurisdiction. Since genotyping results are not automatically shared between TB program jurisdictions, special attention needs to be paid to this possibility.**Drug susceptibility test**
A laboratory test to determine if a *M. tuberculosis* isolate is susceptible to a specific drug used to treat TB.**DNA genotyping**
A laboratory approach that provides a description of the genetic makeup of a *M. tuberculosis* complex isolate.**Endemic strain**
A strain of *M. tuberculosis* that has circulated in a relatively closed population for many years. Patients who are infected with endemic strains are often not involved in the same chain of recent transmission (i.e., within the previous 2 years), even though the genotypes of the isolates from the patients match. (See Braden 1997.)**Epidemiologic cluster**
Two or more persons with TB who share known epidemiologic links. Many scientists use the term “cluster” to refer only to isolates with matching genotypes, but the term “epidemiologic cluster” has become common enough to include as a legitimate term.**Epidemiologically confirmed genotyping cluster**
Genotyping cluster that contains TB patients with known epidemiologic links.**Epidemiologic (Epi) link**
A characteristic that two TB patients share that explains where and when TB could have been transmitted between them. An epidemiologic link could be a location where the two persons spent time together or a relationship that brought them together. A known epidemiologic link is defined as either a) one of the patients named the other as a contact during one of the patient’s infectious period or b) the two patients were at the same place at the same time during one of the patient’s infectious period. A possible epidemiologic link is defined as either a) the two patients spent time at the same place but the timing of when they were there or the timing of the infectious period was not definite enough to meet the criteria for a known epidemiologic link; OR b) the two patients lived in the same neighborhood around the same period of time; OR c) the two patients worked in or were at the same geographic area around the same period of time and shared social or behavioral traits that increased the chances of transmission.**Exposed cohort**
A group of people who shared the same air space with a TB patient during the patient’s infectious period. An outbreak investigation focuses on defining the exposed cohort for infectious TB patients in order to identify contacts that need to be screened for TB and latent TB infection.**False-positive culture**
Cultures or reports of cultures of *M. tuberculosis* that are not accurate. False-positive cultures occur when *M. tuberculosis* bacteria from one specimen, instrument, or culture inadvertently contaminate another specimen or culture or when clerical errors occur and specimens are mislabeled or misreported. Clinical equipment (e.g., bronchoscopes, sputum collection booths, and ultrasonic nebulizers), if inadequately cleaned, can become contaminated and be the source of false-positive cultures. Cross-contamination can occur in the laboratory during batch processing, pipetting, transfer of bacilli from a broth-culture system, work in a faulty exhaust hood, or species-identification procedures.**Fingerprinting**
Refers to TB genotyping using IS*6110*-based RFLP analysis.**Genetic cluster**
Synonym for *Genotyping cluster*.**Genotype**
The designation that results from one or more of the three genotyping techniques used for *M. tuberculosis*: spoligotyping, MIRU analysis, and IS*6110*-based RFLP.**Genotyping cluster**
A group of isolates that share the same genotyping pattern. This term is also applied to the TB patients who produced the isolates with the same pattern. The genotyping laboratories will report a PCR cluster designation for isolates with spoligotypes and MIRU types that match other isolates from the same TB program. The laboratories will report a PCR/RFLP cluster designation for isolates in the same PCR cluster that also have the same RFLP pattern.**Genotyping match**
Two or more *M. tuberculosis* isolates that share the same genotype.**Genotyping**
Also referred to as DNA genotyping. A laboratory approach used to determine if *M. tuberculosis* isolates are genetically related.**H37Rv strain**
The H37Rv *M. tuberculosis* strain is commonly used as a control strain in laboratory assays.**Immunocompromised**
A condition in which the immune system is not functioning normally. According to some style experts, *immunocompromised* is the broader term, and *immunosuppression* is restricted to states with iatrogenic causes, including causes that result from therapy for another condition. Immunocompromised persons are at greatly increased risk for progressing to TB disease after infection with *M. tuberculosis*. Immunocompromised conditions also make TB disease more difficult to diagnosis, increasing the likelihood of a false-negative result for a test for *M. tuberculosis* (e.g., TST).**Index case**
The first TB patient identified in cluster. The index case is not necessarily the source case.**Infectious period**
The time period during which a person with TB disease is considered infectious and capable of transmitting *M. tuberculosis* to persons who share the same air space. See Chapter 4,*******Combining Genotyping and Epidemiologic Data to Improve Our Understanding of Tuberculosis Transmission*, for details.**IS*6110* RFLP**
Insertion sequence *6110* (read “I- S-sixty-one-ten”) is a genetic marker apparently unique to members of the *M. tuberculosis* complex. IS*6110*-based restriction fragment length polymorphism (RFLP) analysis was the first widely used method for genotyping *M. tuberculosis* isolates.**Jurisdiction**
The geographic extent of a TB program’s coverage. The jurisdiction of a county health department is that county.**LTBI**
Latent tuberculosis infection.**Manila strain**
A family of isolates of *M. tuberculosis* found commonly among immigrants from Manila. The spoligotype and MIRU genotype of Manila strain isolates are similar, yet in most cases, patients infected with the Manila strain do not represent recent transmission. IS*6110*-based RFLP is helpful in distinguishing between Manila strain isolates within a PCR cluster.**Matching genotypes**
Two or more *M. tuberculosis* isolates that share the same genotype. See Chapter 4,*******Combining Genotyping and Epidemiologic Data to Improve Our Understanding of Tuberculosis Transmission*, for more information.**MDR and MDR TB**
Multidrug-resistant and multidrug-resistant tuberculosis. *M. tuberculosis* strains that are resistant to at least isoniazid (INH) and rifampin.**MIRU**
Mycobacterial interspersed repetitive unit analysis (read “MIR-ooh”). MIRU is a PCR-based genotyping assay. The CDC genotyping program requires the regional genotyping laboratories to perform MIRU analysis on every isolate submitted. See Chapter 3,*******CDC Tuberculosis Genotyping Laboratory Procedures*, for more information.***M. tuberculosis* complex**
****Often abbreviated *MTC*, a group of closely related mycobacterial species that can cause LTBI and TB disease (i.e., *M. tuberculosis, M. bovis, M. africanum, M. canetti, M. microti, and the* BCG strain). Most TB in the United States is caused by *M. tuberculosis.***Nonmatching genotype**
An isolate that has a unique genotype (i.e., a genotype pattern that does not match the pattern of any other isolate in a TB program’s database).**Nontraditional setting**
A setting where TB transmission took place that is not considered a traditional transmission setting, such as the home or workplace. Common nontraditional transmission settings identified during cluster investigations have included bars and social clubs, churches/temples, and drug/crack houses.**Nonviable cultures**
Organisms that can no longer be grown in culture. Genotyping techniques that are based on the PCR test can by performed on nonviable cultures. IS*6110*-based RFLP, on the other hand, requires viable cultures that can be grown until they provide sufficient material.**NTCA**
National Tuberculosis Controllers Association.**NTGSN**
National Tuberculosis Genotyping and Surveillance Network. This network was established by CDC in 1996 to assess the utility of molecular genotyping for improving tuberculosis prevention and control. The NTGSN study included seven laboratories and seven sentinel surveillance sites in the United States. Sentinel surveillance sites included the states of Arkansas, Maryland, Massachusetts, Michigan, and New Jersey and six counties in California (Alameda, Contra Costa, Marin, San Mateo, Santa Clara, and Solano); and four counties in Texas (Dallas, Tarrant, Cameron, and Hidalgo).**Octal designation**
To simplify the recording of the results of spoligotyping, the results are given as an octal representation. The octal designation uses base 8, which contains the numbers 0–7. Any spoligotyping banding pattern can be converted to an octal designation, and any octal designation can be converted back to give the original hybridization pattern. See Chapter 3, *CDC Tuberculosis Genotyping Laboratory Procedures*, for details.**Outbreak**
An increase in the number of TB cases in time and space over that which is expected. See Chapter 6,*******Applying Genotyping Results to Tuberculosis Control Practices*, for more information.**Outbreak investigation**
An investigation of an outbreak with the goals of a) identifying and treating all cases of active TB so that transmission stops and b) identifying all cases of LTBI that would benefit from treatment and assuring that it is completed so the outbreak does not continue in the future.**PCR**
Polymerase chain reaction. The CDC genotyping program uses two PCR-based techniques — spoligotyping and MIRU analysis. Only a small amount of culture is needed for PCR-based genotyping, and the PCR test can be completed in 1day (because the PCR tests are batched, the actual turn-around time from receipt of a specimen to reporting the results can be longer).**PCR cluster designation**
The genotyping laboratories will assign a PCR cluster designation to *M. tuberculosis* isolates that have matching genotypes by the two PCR tests, spoligotyping and MIRU analysis. See Chapter 4,*******Combining Genotyping and Epidemiologic Data to Improve Our Understanding of Tuberculosis Transmission*, for details.**PCR/RFLP cluster designation**
The genotyping laboratories will assign a PCR/RFLP cluster designation to *M. tuberculosis* isolates that belong to the same PCR cluster and are demonstrated to have the same RFLP pattern. See Chapter 3,*******CDC Tuberculosis Genotyping Laboratory Procedures*, for details.**Recent transmission**
The transmission of TB that has occurred in the recent past, as opposed to reactivation of a latent TB infection. Although the precise time period that distinguishes TB that resulted from “recent” transmission and TB that resulted from reactivation of a latent infection is not well defined, “recent” transmission is often considered to be within the last 2 years.**Reinfection vs. relapse**
A case of relapsed TB represents a worsening of an infection after a period of improvement and is caused by the same strain of *M. tuberculosis*. TB that represents a reinfection is caused by a second infection with a strain that is different from the strain that caused the initial infection. Genotyping the initial and the subsequent *M. tuberculosis* isolate can distinguish these two possibilities.**RFLP**
Restriction fragment length polymorphism. A genotyping technique based on measuring the number and length of specific DNA fragments that are cut using specific restriction enzymes. The RFLP technique used to genotype *M. tuberculosis* is based on the IS*6110* insertion sequence.**RVCT**
Report of a Verified Case of TB. National surveillance data on patients with tuberculosis is recorded onto this report form.**Selective genotyping**
The process of submitting only selected isolates for genotyping. Because of the cost of submitting all isolates for genotyping (i.e., “universal genotyping”), some programs may initially have to select only high-priority isolates to be submitted for genotyping. See Chapter 5, *Developing a Tuberculosis Genotyping Program*, for more information.**Source patient**
A patient with infectious TB who is thought to be the source of another patient’s TB infection. Also referred to as the source case.**Spoligotyping**
Spacer oligonucleotide genotyping. A genotyping technique based on spacer sequences found in the direct repeat region in the *M. tuberculosis* chromosome. See Chapter 3, *CDC Tuberculosis Genotyping Laboratory Procedures,* for more information.**Traditional settings**
Usual or suspected settings for TB transmission, such as the home or workplace. See also *Nontraditional setting.***TST**
Tuberculin skin test.**Unique genotype**
A genotype designation that does not match that of any other isolate in a TB program’s database.**Universal genotyping**
The policy of submitting all *M. tuberculosis* isolates for genotyping. See Chapter 5, *Developing a Tuberculosis Genotyping Program*, for more information.**VNTR**
Variable number tandem repeat analysis. VNTR is a type of MIRU analysis. See also *MIRU*.
							
					
						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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