Guide to the Application of Genotyping to Tuberculosis Prevention
CDC Tuberculosis Genotyping Laboratory Procedures
Submission of Isolates
TB Genotyping Isolate Submission Form
The submitting laboratory will be responsible for completing the
TB Genotyping Isolate Submission Form when they submit isolates
to the genotyping laboratory. An electronic copy of this Excel spreadsheet
form is available for downloading from the TB WebBoard at
It is absolutely critical that TB programs and laboratories NOT
change in any way the column headings of the Isolate Submission
form spreadsheet. Any change in the column headings will result
in data being lost.
The spreadsheet contains three optional columns (the column headings
are “option_1”, “option_2” and “option_3”), which the TB programs
can use to record any information they want, but they must
not change the column headings for these fields either. For example,
the column labeled as “option_1” could be used to record the zip
code of patients, but the heading must remain “option_1” on the
submitted form. Any optional columns that the program does not want
to use can be deleted, and the order of the columns on the form
can be changed to suit the program.
Guidelines for Submission
The TB Genotyping Isolate Submission Form is an Excel spreadsheet,
and laboratories that can use Excel should enter the isolate information
directly onto the spreadsheet. One spreadsheet line should be used
for each isolate. List all of the isolates that will be shipped
in one container on one spreadsheet; print and insert a copy of
the spreadsheet into the container. In addition to mailing a hard
copy of the spreadsheet with the isolates, send a copy of the Excel
spreadsheet as an e-mail attachment to the genotyping laboratory.
Send a courtesy copy to the state TB program for matching with the
TB program’s list of new cases and with later genotyping results.
Patient confidentiality must be protected, but sufficient patient
identification data are needed to allow this reconciliation to occur
Special procedures will be required for submitting laboratories
that do not have access to Excel. They should
- enter the required information onto a sheet of paper, using
a separate sheet for each patient and
- mail these pages and a packing list of all the isolate identification
numbers with the isolates.
Submitting laboratories that can use Excel but cannot e-mail Excel
attachments should print out hard copies of the Excel spreadsheet
and mail them to the genotyping laboratory.
Upon receipt of the isolates, the genotyping laboratory will match
the isolates that arrive in the shipment with the printed copy of
the spreadsheet that accompanies the shipment. If all of the isolates
are accounted for, the genotyping laboratory will acknowledge receipt
to the submitting laboratory by e-mail; a courtesy copy will be
sent to the TB program. For submitting laboratories that cannot
receive acknowledgement by e-mail, the genotyping laboratory will
mail a hard copy acknowledgement. Isolates will be assigned genotyping
laboratory accession numbers that will include the year, consecutive
numbers, and a letter code that represents the genotyping laboratory
Material for Isolate Submission
Because only small amounts of culture material are required for
the PCR-based typing methods, submitting laboratories should prepare
an isolate for shipment as soon as it is identified as M. tuberculosis
complex (including M. bovis and Mycobacterium africanum).
Portions of the culture material should be placed in 2-ml screw-cap
vials, which will provide substantial savings in shipping costs.
Although the process of subculturing onto Lowenstein-Jensen (L-J)
medium (waiting 3 weeks for visible growth and then shipping the
L-J slant) is acceptable, it greatly delays turnaround times and
substantially increases shipping costs.
The genotyping laboratory will subculture submitted material for
possible IS6110-based RFLP typing and long-term storage.
Isolates that do not grow on subculture at the genotyping laboratory
will be typed by spoligotyping and MIRU, and replacements for these
non-viable isolates will be requested from the submitting laboratory.
Acceptable Material for Isolate Submission
- Portions of culture material from solid medium transferred
to 2-ml screw-cap vials
- Samples (0.5-1.0 ml) of broth culture transferred to vials
- Portions (0.5-1.0 ml) of broth cultures or suspensions prepared
for susceptibility testing
- Suspensions (0.5-1.0 ml) prepared for Accuprobe testing (before
- L-J (or other solid medium) slants or bottles (not optimal;
see discussion in the previous section, Material for Isolate
Unacceptable Material for Isolate Submission
- Clinical specimens (e.g., sputum, pleural fluid)
- Sediments from processed clinical samples, regardless of smear
or nucleic acid amplification positivity
- Petri plates
- Cultures not yet identified as M. tuberculosis complex
- Obviously contaminated or suspected mixed cultures
- Each sample must be labeled clearly with a patient identifier,
and the same patient identifier must be listed on the TB Genotyping
Isolate Submission Form.
- Liquid samples should be shipped in plastic screw-cap tubes
with o-rings. The tubes should be surrounded by absorbent material.
- Containers and labels must comply with all regulations of the
U.S. Department of Transportation and the International Air Transport
Association for shipment of infectious material.
- Shipping personnel should have completed required training.
- See Information on Packaging and Shipping Infectious Substances
in Appendix B, under Useful Resources, for additional information.