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BACKGROUND: The New York City (NYC) Department of Health and Mental Hygiene Bureau of Tuberculosis Control (BTBC) began universal genotyping in 2001 using IS6110-based restriction fragment length polymorphism (RFLP) analysis and spacer oligonucleotide typing (spoligotyping) to identify tuberculosis (TB) strains and better understand TB transmission through genotype cluster identification. The Centers for Disease Control and Prevention (CDC) implemented universal genotyping nationally in 2004 and has used spoligotyping and 24-loci mycobacterial interspersed repetitive unit analysis (MIRU24) to define genotype clusters since 2009. We analyzed our genotype results to characterize TB strains and examine consistency of clustering across multiple available genotyping methods in NYC.
METHODS: Available genotyping results were reviewed and described for all culture-positive TB cases counted in NYC between January 1, 2001, and December 31, 2012. We defined a NYC cluster as two or more cases with identical spoligotype and RFLP patterns and a CDC cluster as two or more cases counted since 2009 with identical spoligotype and MIRU24 patterns.
RESULTS: Among 10,991 TB cases counted in NYC from 2001-2012, 8,300 (76%) were culture-positive. Of these, 7,777 (94%) had RFLP and spoligotype results available. During the study period, 1,304 unique spoligotypes and 4,687 unique RFLP patterns were identified. Among cases with spoligotype and RFLP results available, 3,386 (44%) were clustered in 744 NYC clusters (cluster size range: 2-202 cases; median: 2). Among 1,927 (97%) culture-positive cases counted since 2009 with MIRU24 results available, 1,487 unique MIRU24 patterns were identified. Among 1,805 cases counted since 2009 with RFLP, spoligotype, and MIRU24 results available, 504 (28%) cases were clustered in 155 NYC clusters, and 521 (29%) cases were clustered in 166 CDC clusters. Among NYC clusters, 84 (54%) were associated with multiple MIRU24 patterns (range per cluster: 1 to 15 MIRU24 patterns). Among CDC clusters, 76 (46%) were associated with multiple RFLP patterns (range per cluster: 1 to 13 RFLP patterns).
CONCLUSIONS: In this large sample of TB cases spanning 12 years of universal genotyping, high strain diversity was observed. Most culture-positive cases had spoligotype and RFLP results available, and 56% of genotypes identified were unique. In a subset of cases counted since 2009 with all genotype results available, more than half of NYC clusters were associated with multiple MIRU24 patterns, while 43% of CDC clusters were associated with multiple RFLP patterns. Further analysis of differences in clustering across genotyping methods is warranted.