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No. 4, 2008

Mycobacteriology Laboratory Branch Updates

Award of Genotyping Contracts

The Mycobacteriology Laboratory Branch (MLB) is pleased to announce the recent award of two contracts for the continuation of the U.S. National Tuberculosis Genotyping Service (NTGS). The contracts have been awarded to Dr. James Rudrik and his staff at the Michigan Department of Community Health in Lansing, Michigan, and to Dr. Ed Desmond and his staff at the California Department of Health in Richmond, California. The laboratory workers at these sites have extended experience in genotyping Mycobacterium tuberculosis. In the early 1990s, these sites served as regional laboratories providing IS6110-RFLP for suspected outbreaks and false-positive culture investigations. From 1996 to 2000, both laboratories participated in the National TB Genotyping and Surveillance Network. In 2003, they were awarded the original NTGS contract and have provided access to universal genotyping services to all TB control programs in the United States. Since the inception of this program, these laboratorians have genotyped more than 39,000 isolates. Their extensive experience and institutional knowledge of M. tuberculosis genotyping in the United States makes them exceptional partners for continuing the NTGS for the next 5 years.

Launch of Expanded Genotyping Assay

MLB is also pleased to announce an improved method for genotyping M. tuberculosis. Instrumentation is being shipped to the NTGS contractors that will allow them to increase their throughput and also to perform an expanded mycobacterial interspersed repetitive units–variable number tandem repeat (MIRU-VNTR) assay. The original assay was based on the determination of the number of repeated units at 12 separate loci within the M. tuberculosis genome. The expanded assay will determine the number of repeated units at 24 loci — the original 12 loci and 12 new loci (hereafter referred to as MIRU1 and MIRU2, respectively). This expanded assay has been reported to reach the level of discrimination of IS6110-RFLP fingerprinting (Oelemann et al.  J Clin Microbiol 2007; 45:691-697), and data generated in MLB suggest that it will divide some large clusters into smaller, and potentially more meaningful, clusters. The expected launch date of this additional typing assay was January 1, 2009. Starting at that time, all isolates submitted to the NTGS are being typed using spoligotyping, MIRU1, and MIRU2 assays. 

Frequently Asked Questions on the Expanded Genotyping Assay
“How will this change affect my current database?” Continuity between the current genotyping approach and the new genotyping approach is critical. Spoligotype and MIRU1 fields will be reported as in the past. PCR types and state cluster names will continue to be based on spoligotype and MIRU1. MIRU2 results will be reported in a new field in the genotyping report sent to TB programs and will be used to subcluster the original PCR types and state cluster names. A new fact sheet describing this in detail will be distributed to TB control programs.

“Will I be able to request MIRU2 typing for some of our older isolates?” Yes. All isolates submitted for genotyping prior to January 2009 and their DNA preparations will be stored at CDC. You may request MIRU2 typing from CDC by following the guidelines for requesting IS6110-RFLP fingerprinting. However, conducting MIRU2 typing for all isolates collected prior to 2009 (approx. 39,000 isolates) would be unrealistic. Therefore, programs must demonstrate the need for further characterization based on public health impact, such as the need to conduct a cluster investigation, for which additional typing information might be useful.

“Will IS6110-RFLP fingerprinting continue to be available?” Yes. There will be no change in the mechanism or basis for requesting IS6110-RFLP fingerprinting from the genotyping contract labs.

We hope that you are looking forward to this major improvement as much as we are, but we also know that you may have questions and concerns. Your input is invaluable to us as we make this transition and we look forward to receiving your comments (

—Reported by Lauren S. Cowan, Ph.D.
NTGS Project Officer
Mycobacteriology Laboratory Branch
Div of TB Elimination


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