National Tuberculosis Genotyping and Surveillance Network: Analysis of the Genotype Database

As part of the National Tuberculosis and Genotyping Surveillance Network, isolates obtained from all new cases of tuberculosis occurring in seven geographically separate surveillance sites from 1996 through 2000 were genotyped. A total of 10,883 isolates were fingerprinted by the IS6110-restriction fragment length polymorphism method, yielding 6,128 distinct patterns. Low-copy isolates (those with six or fewer bands) were also spoligotyped. The distribution of specific genotype clusters was examined. Databases were also examined for families of related genotypes. Analysis of IS6110 patterns showed 497 patterns related to the W-Beijing family; these pattens represent 946 (9%) of all isolates in the study. Six new sets of related fingerprint patterns were also proposed for isolates containing 6–15 copies of IS6110. These fingerprint sets contain up to 251 patterns and 414 isolates; together, they contain 21% of isolates in this copy number range. These sets of fingerprints may represent endemic strains distributed across the United States.