Guide to the Application of Genotyping to Tuberculosis Prevention and Control

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. IS6110-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 IS6110-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 IS6110-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.
IS6110 RFLP	Insertion sequence 6110 (read “I- S-sixty-one-ten”) is a genetic marker apparently unique to members of the M. tuberculosis complex. IS6110-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. IS6110-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. IS6110-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 IS6110 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