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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