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Table 1 Sequenced Mtb Fingerprinting or Epidemiological Clusters

From: Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

Cluster Name Cluster Family # of Isolates # of WGS Isolates # of SNP Loci in Cluster SNP Range Transmission Linked?
Large Clusters Identified by Identical Genetic Fingerprints
 Manila Cluster 1 Manila 23 3 178 73–148 No
 Manila Cluster 2 Manila 24 2 161 No
 Beijing Cluster 1 Beijing 11 4 63 0–52 Partial
 Beijing Cluster 2 Beijing 7 7 0 Yes
Clusters Identified by Shared Uncommon Spoligotypes
 Manila-like Cluster 1 Manila 2 2 3 Yes
 Manila-like Cluster 2 Manila 2 2 4 Yes
 Beijing Cluster 5 Beijing 2 2 1 Yes
 Manila-like Cluster 3 Manila-like 3 3 3 1–3 Yes
 H3 Cluster 1 H3 3 (1) 3 1230 3–1230 Partial
Epidemiologically Identified Putative Clusters
 Manila Cluster 3 Manila 2 2 90 No
 Manila Cluster 4 Manila 2 2 0 Yes
 Manila Cluster 5 Manila 2 2 192 No
 Manila Cluster 6 Manila 2 2 229 No
 Beijing Cluster 3 Beijing 2 2 3 Yes
 Mixed Cluster 2 U/Beijing 2 2 1153 No
 U Cluster 1 U 4 4 131 1–117 Partial
 Mixed Cluster 1 Beijing/Manila 3 3 1762 1–1762 Partial
 Manila Cluster 7 Manila 2 2 142 No
 Beijing Cluster 4 Beijing 2 2 0 Yes
  1. # of WGS Isolates is the number of isolates from each cluster that were sequenced with Illumina whole genome sequencing. # of SNP Loci in Cluster is the total number of SNP loci possessing alleles that differentiate isolates within the cluster. SNP Range lists the smallest and largest numbers of SNPs between any two isolates in the cluster. Transmission Linked is marked as “No” if all isolates in the cluster differ by 12 SNPs or more, “Yes” if they differ by 5 SNPs or fewer, or “Partial” if some, but not all, isolates within the cluster differ by 5 SNPs or fewer. H3 Cluster 1 includes a fourth isolate that was not available for sequencing. Clusters are listed in the order in which they are discussed in the text