Guide to the Application of Genotyping to Tuberculosis Prevention and Control

Developing a Tuberculosis Genotyping Program

Initial Decisions

Clarifying Activities and Assigning Responsibilities

A TB genotyping program plan will involve many persons from many organizations working together. It will be helpful if activities and responsibilities are clarified at the beginning. Table 5.2 lists some key activities and provides suggestions about which groups may be responsible for each activity.

Table 5.2. Suggested activities and responsibilities for TB genotyping programs.

Activities Responsibility
Establishing a TB Genotyping Program Plan Usually, this will be done by the state/large city TB program. In unusual circumstances, and with prior approval of the state TB program, a city that does not have a cooperative agreement with CDC may submit a plan for approval.
Deciding on initial scope of isolate submission:
a) only selected isolates; b) all isolates in state;
c) all isolates from predefined geographic area
State/large city TB program
Clarifying roles and assigning responsibilities State/large city TB program
Submitting isolates to the genotyping laboratories for genotyping Public health laboratories and/or clinical laboratories will submit isolates. The state/large city TB program will provide instructions on how this is to be done.
Performing genotyping and reporting results to the TB program Genotyping laboratory
Managing genotyping database and tracking isolates that are submitted for genotyping State/large city TB program
Receiving and recording genotyping laboratory reports State/large city TB program
Responding to genotyping results State/large city and local TB programs
Providing genotyping technical consultations Genotyping laboratory and CDC
Providing epidemiologic consultations State/large city TB program and CDC

Deciding on Initial Scope of Genotyping Program: Three Options

Universal genotyping (i.e., submitting all isolates from a TB program to the genotyping laboratories) holds great promise for improving TB control. We believe that, within the next few years, programs will want to have all their M. tuberculosis complex isolates genotyped, just as they now have all their isolates analyzed for drug susceptibility patterns. However, for programs to implement a genotyping program, they will have to invest additional resources to pay for shipping the isolates to the genotyping laboratories. Programs may also have to hire additional staff or assign new duties to existing staff so they are able to administer the program and respond to newly identified genotyping clusters. Thus, initially, some programs will not be able to implement universal genotyping.

There are three options for selecting the isolates that will be submitted to the genotyping laboratories for genotyping.

Option 1: Universal submission of isolates program-wide
This option involves submitting one isolate from every patient with a culture-positive specimen in a TB program’s jurisdiction.

Advantages of universal genotyping. This option provides the greatest benefit. Universal program-wide genotyping provides the best understanding of the epidemiology of tuberculosis transmission within the entire TB program’s jurisdiction and uncovers the greatest number of unexpected outbreaks, clusters, and false-positive cultures.

Disadvantages of universal genotyping. This is the most expensive option, and it requires a substantial commitment of resources.

Option 2: Universal submission of isolates from a selected subregion
In this option, a specific geographic area is selected (e.g., a particular county TB program or several adjacent county programs), and all isolates that come from patients in the area are submitted.

Advantages of universal genotyping in a subregion. This option provides all the benefits of universal program-wide genotyping as they apply to the specific region. It will be more manageable than a program-wide effort. After a county universal genotyping program is set up and running well, the program may be expanded to other counties or to an entire state.

Disadvantages of universal genotyping in a subregion. The full benefits of universal program-wide genotyping will not be realized. If a TB program decides to adopt Option 3, the following questions should be considered in selecting county TB programs to participate:

  • Is there buy-in from the county TB programs?
  • Can isolate submissions be coordinated easily? (It will be easier to work with a county where most isolates can be submitted by one laboratory than with a county where isolates would be submitted by multiple laboratories.)
  • If more than one county will participate, are the counties contiguous?
  • Do the counties have a large number of TB cases? (Although it may be easier to start in a county with a small number of cases, the benefit will be greater in a county with many cases.)
  • Does TB occur often in high-risk populations in the counties of interest?

Option 3: Selective submission of isolates
A policy of selective submission is a decision by the TB program to submit only those M. tuberculosis isolates that meet certain criteria. This option allows programs that cannot implement universal genotyping to take advantage of the services of the genotyping laboratory. For example, if the TB program suspects that several TB cases are involved in the same chain of recent transmission, isolates from these patients can be submitted to the genotyping laboratory. Similarly, if a TB program or a laboratory suspects that a diagnosis of TB is the result of a false-positive culture, the isolate from the diagnosed case-patient and the isolate that might have been identified as the possible source of the false-positive culture can be submitted for genotyping.

Advantages of selective genotyping. It saves shipping costs because only high-priority isolates are submitted. The selective submission option will also minimize the number of times a TB program will need to conduct a cluster investigation, because the TB program will submit for genotyping only those isolates from high-priority suspected clusters.

Disadvantages of selective genotyping. First, selective genotyping does not allow a TB program to realize the full benefit of genotyping. Because only selected isolates are genotyped, the TB program will be less likely to learn about unsuspected recent transmission. With selective genotyping, you can confirm only what you already suspect. For similar reasons, the discovery of unsuspected false-positive cultures, which is one of the most important benefits of universal genotyping, is not possible with selective genotyping.

The second disadvantage of selective genotyping is that it requires several steps to locate and request submission of isolates; these steps are not necessary with universal genotyping. For example, under a policy of selective submission, if an outbreak is suspected and a TB program wants to submit isolates from the patients who are considered part of the outbreak, the TB program must determine which patients have culture-positive isolates and what laboratories have those isolates. The TB program must send a request to the laboratories; the laboratories must locate and possibly subculture the isolates before they can be sent to the genotyping laboratories. With universal genotyping, all isolates are submitted automatically for genotyping; no person at the TB program would need to identify isolates for genotyping or to make an individual request to the laboratories, and the laboratories might have prepared an isolate for shipment as a routine part of their procedures for processing cultures.

Summing Up: Deciding on Initial Scope of Genotyping Program

One of the first decisions a TB program must make is the initial scope of their genotyping program. There are three options:

Universal genotyping program-wide provides the most benefit, but it requires a substantial investment in program resources.

Universal genotyping for a subregion (a single county or adjacent county TB programs) provides some of the benefits of statewide universal genotyping but is easier to initiate and costs less.

Selective genotyping is the easiest to initiate and the least expensive.

Identifying Laboratories that Will Submit Isolates to the Genotyping Laboratories

The TB program that opts for universal genotyping, either program-wide or within a particular county, needs to identify the laboratories in their jurisdiction that will submit M. tuberculosis isolates to their genotyping laboratory. The TB program that opts for selective genotyping may wait to contact submitting laboratories until the program identifies specific isolates to be submitted.

If all M. tuberculosis isolates are sent to the state public health laboratory for routine isolation and identification or for drug susceptibility testing, it will be easier to have that laboratory be responsible for submitting isolates to the genotyping laboratory. If the state public health laboratory does not receive all isolates, the TB program should explore the feasibility of establishing a new state health regulation that calls for all M. tuberculosis isolates to be submitted to the state laboratory. The regulatory language used by the New York City TB program to have all isolates submitted to their public health laboratory is available for review on the WebBoard at

If a new regulation is not feasible or is delayed, and the state public health laboratory cannot be the only entity that will submit isolates to the genotyping laboratory, a process will have to be implemented to identify the laboratories that isolate and identify M. tuberculosis from patients in the state or county. This will include state and county public health laboratories, private laboratories, large commercial laboratories (which may include out-of-state laboratories), and laboratories at medical centers and hospitals.

Laboratories perform various types of services. For the purpose of submitting isolates, only laboratories that identify isolates as M. tuberculosis complex should be considered. Laboratories that isolate mycobacteria but do not process them further do not have to be considered, although such laboratories may be conduits for reporting results to clinicians or to the TB program.

Many laboratories isolate and identify M. tuberculosis and then send the isolates to a state or reference laboratory for susceptibility testing. In these cases, either the originating or reference laboratory could be designated as the entity to submit isolates for genotyping. Asking the originating laboratory to submit isolates will provide the most rapid turnaround, but this will require the originating laboratory to ship the isolate twice: once to the reference laboratory and once to the genotyping laboratory. Many laboratories may find this unworkable.

The Division of Laboratory Systems at CDC developed the National Laboratory Database (NLD) of all Clinical Laboratory Improvement Amendments (CLIA)-approved laboratories in the United States. CDC provides access to this database to all 50 state public health laboratory directors. One of the variables is mycobacteriology, which allows a state public health laboratory director to download a list of every laboratory that performs some level of mycobacteriology testing. The system also allows the state laboratory director to download an accurate mailing list of these laboratories. TB programs that want to use the NLD should request approval from their state laboratory director, asking that the director grant NLD access to a specific person by sending an email to Dr. Rex Astles at

Establishing a Communications Plan

Effective communication among the state and local TB programs, state laboratory, submitting laboratories, and the genotyping laboratory is critical to the success of genotyping. Planning for an effective communications system should be one of the initial steps in developing a genotyping program. The system (e.g., a shared web-based database, e-mail, telephone, or fax) will depend on local capabilities. Approaches to ensure that patient confidentiality is maintained should be addressed.