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No. 2, 2012


TB Genotyping Updates from DTBE Molecular Epidemiology Activity

The Molecular Epidemiology Activity (MEA) in DTBE’s Surveillance, Epidemiology, and Outbreak Investigations Branch has recently developed several new products that we believe will help state, local, tribal, and territorial TB programs effectively use genotyping data.

GENType: a New TB Genotyping Terminology
The National TB Genotyping Service (NTGS) has been defining genotypes using the term “PCRType,” which is assigned for each unique combination of spoligotype and 12-locus MIRU-VNTR results, and is designated as ‘‘PCR’’ followed by five digits (e.g., PCR00002). However, in April 2009, MIRU-VNTR analysis was expanded from 12 loci to 24 loci (24-locus MIRU-VNTR). The additional information increases our ability to discriminate among chains of transmission and makes TB genotyping even more useful for routine TB control.

In order to fully integrate 24-locus MIRU-VNTR into routine use, a new national naming system, GENType, has been developed and integrated into the TB Genotyping Information Management System (TB GIMS). Each unique combination of spoligotype and 24-locus MIRU-VNTR results has been assigned a GENType, formatted as “G” followed by five digits. For example, G00010 refers to the unique combination of spoligotype: 000000000003771 and 24-locus MIRU-VNTR: 223325173533 444534423428. The GENType Fact Sheet has more information about the new terminology.

Expanding 24-locus MIRU-VNTR Availability for 2009 Isolates
Most TB isolates that were genotyped prior to April 2009 do not have complete 24-locus MIRU-VNTR data. MEA is working with DTBE’s Laboratory Branch (LB) to obtain complete MIRU-VNTR results for all 2009 isolates. This information will improve our understanding of genotype clusters and help TB control staff integrate GENType into their routine work.

2010 Annual Genotyping Report
TB genotyping has come a long way since NTGS was started in 2004. We are celebrating our progress by publishing the first ever Annual Genotyping Report, Tuberculosis Genotyping in the United States, 2004-2010. Much like the annual TB surveillance report, this report summarizes some key data regarding TB genotyping in the United States, including the substantial progress TB programs have made in increasing TB genotyping surveillance coverage (from 51.3% in 2004 to 88.2% in 2010).

Best Practices for Genotyping-Based Tuberculosis Outbreak Detection
The Outbreak Detection Working Group, a multi-agency work group of partners with expertise in TB control and genotyping, has developed a document that outlines six best practices regarding the use of TB genotyping in routine TB control activities. These best practices are meant to be a tool for programs to reference as they develop their genotyping programs; they do not represent mandatory activities under any currently established CDC cooperative agreements, grants, or contracts. Within the document, the practices are listed in order of importance; each is followed by a list of activities that support that best practice.

The best practices are

  1. Ensure each patient with a positive TB culture result has a genotyped isolate;
  2. Link genotyping results to surveillance data promptly;
  3. Integrate genotyping information into routine case management, contact investigation, and cohort review activities;
  4. Examine concerning genotype clusters;
  5. Communicate with other jurisdictions and CDC; and
  6. Develop and maintain capacity for using genotyping information in routine TB control.

A factsheet on best practices for genotyping is available on the CDC TB website.

The webinar “Best Practices in Genotyping-Based Tuberculosis Outbreak Detection” was presented on May 24, 2012. Some TB control staff were not able to participate; however, we recorded the presentation so that it can be viewed at a later date. You do not need to register to access the recording. Simply enter your name on the first screen, and click “Submit.” You will then be taken directly to the webinar. The recording will be available for at least a year.

Have questions about TB genotyping?
Your state, tribal, or territorial TB program is the best first stop for more information about TB genotyping. If you’re not sure of the correct person to contact, or you are in a state, tribal, or territorial TB program, e-mail with your question. Someone from MEA will answer it, or we will find out who in your state or territory you can contact.

—Reported by Juliana Grant, MD
Div of TB Elimination

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