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U.S. Department of Health and Human Services


Guide to the Application of Genotyping to Tuberculosis Prevention and Control

Combining Genotyping and Epidemiologic
Data to Improve Our Understanding of
Tuberculosis Transmission

Reading the Genotyping Laboratory Report

Table 4.3 is a mock-up of some of the information that the genotyping laboratory report will contain when the laboratory transmits genotyping results to TB programs (actual reports contain additional information). For this example, we have assumed that these data are being reported to the “XY” State TB program. This mock-up report will be used to demonstrate the interpretation of genotyping results.

The genotyping laboratory accession numbers are assigned by the genotyping laboratory to isolates as they are received from all programs. The first two digits in the accession number indicate the calendar year, the two letters indicate which of the two genotyping laboratories performed the typing, and the last four numbers are consecutive. The date received indicates the actual date the isolates were received at the genotyping laboratory.

The spoligotype is the 15-digit octal designation for the spoligotype. The MIRU type is the 12-character result representing the copy number at the 12 MIRU loci. Note that letters and dashes may be used in these designations in addition to numbers. See Chapter 3, CDC Tuberculosis Genotyping Laboratory Procedures, for details about how spoligotype and MIRU designations are derived.

The PCR cluster designation represents isolates from the same TB control program that have identical spoligotypes and MIRU types. If the isolate does not match any other isolate in the database, no cluster designation is listed. Isolate 03AA2621 matched a previously defined cluster (XY004) and is added to that cluster. Since other isolates in the cluster have been reported previously, they are not included on this report. Isolate 03AA2619 matched isolate 03AA1422 (date received 6/16/03), which was typed previously but was not clustered when first reported. The two isolates were assigned to a new cluster, designated XY025. Although the spoligotype and MIRU type for isolate 03AA1422 were reported previously (date reported 6/22/03), the result is updated to include the new cluster designation, reflected in the date clustered of 12/12/03.

Table 4.3. Sample genotyping laboratory report.*

TB program name Genotyping laboratory accession number Date received Spoligotype MIRU type PCR cluster design-
Date clustered Date reported
XY 03AA2615 12/05/03 777777607760771 123326133227     12/12/03
XY 03AA2616 12/05/03 776377777760771 233426163234     12/12/03
XY 03AA2617 12/05/03 700000007760771 234325153323     12/12/03
XY 03AA2618 12/05/03 677737607760771 224226143321     12/12/03
XY 03AA2619 12/05/03 776377777760771 233326163224 XY025 12/12/03 12/12/03
XY 03AA1422 06/16/03 776377777760771 233326163224 XY025 12/12/03 06/22/03
XY 03AA2620 12/05/03 703707740003771 226425173533     12/12/03
XY 03AA2621 12/05/03 777777777760771 223125153326 XY004 12/12/03 12/12/03
XY 03AA2622 12/05/03 677777607760771 234325153323     12/12/03

*Actual report will contain additional information. See text for details.

Table 4.4 is a mock-up of some of the information contained in the report of IS6110-based RFLP results. The isolates are identified by the genotyping laboratory accession number. No other patient data is needed, since it will be in the previous PCR result report.

In this example, seven isolates of PCR cluster XY004 have been typed by IS6110 RFLP. The first two isolates have been assigned to PCR/IS6110 cluster XY004A. That means that they have the same spoligotype, MIRU type, and identical IS6110 RFLP patterns. Isolates 3-5 are assigned to cluster XY004B, which means they have identical IS6110 RFLP patterns but are different from the first two isolates. The last two isolates do not match any of the others and thus are not assigned to a PCR/IS6110 cluster. All the isolates are assigned an RFLP pattern designation, which consists of the genotyping laboratory accession number and a dash followed by the number of bands in the RFLP pattern (14, 13, or 10 in these examples). For clusters, the designation for the isolate with the earliest accession number is used for all isolates.

Isolate 03AA1857 differs from the isolates in cluster XY004B by the addition of a single band in the RFLP pattern. Since it is not identical, it is not included in the cluster, but the similarity is noted in the comments field. The band number is included in the pattern designation as additional information. Note that isolates having the same band number can have entirely different patterns. Some programs consider isolates differing by only a single RFLP band to be part of a genotyping cluster, which warrants inclusion in any subsequent cluster investigation. Others do not include such isolates in cluster investigations. All should recognize that genotype patterns can change over time due to natural mutations, and cases whose isolates differ by one RFLP band should not be excluded if epidemiologic links indicate the cases are related.

Table 4.4. Sample genotyping laboratory report showing IS6110-based RFLP results.

Genotyping lab accession number

PCR cluster designation

RFLP pattern designation

PCR/RFLP cluster designation

Date reported


03AA0046 XY004 03AA0046-14 XY004A 01/12/04  
03AA2621 XY004 03AA0046-14 XY004A 01/12/04  
03AA0364 XY004 03AA0364-13 XY004B 01/12/04  
03AA0533 XY004 03AA0364-13 XY004B 01/12/04  
03AA1215 XY004 03AA0364-13 XY004B 01/12/04  
03AA1648 XY004 03AA1648-10   01/12/04  
03AA1857 XY004 03AA1857-14   01/12/04 Differs from cluster XY004B by 1 band


Released October 2008
Centers for Disease Control and Prevention
National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
Division of Tuberculosis Elimination -

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