Description of 40 shared-types (SITs; n = 87 isolates) and corresponding spoligotyping defined lineages/sublineages starting from a total of 103 M. tuberculosis strains isolated in Santiago, Chile.

* A total of 39/40 SITs containing 85 isolates matched a preexisting shared-type in the database, whereas 1/40 SIT (n = 2 isolates) was newly created. A total of 13/40 SITs containing 60 isolates were clustered within this study (2 to 11 isolates per cluster) while 27/40 SITs containing 27 strains were unique (for total unique strains, one should add to this number the 16 orphan strains, which brings the number of unclustered isolates in this study to 43/103 or 41.75%, and clustered isolates to 60/103 or 58.25%). Note that SIT followed by an asterisk indicates “newly created” SIT due to 2 or more strains belonging to an identical new pattern within this study or after a match with an orphan in the database; SIT designation followed by number of strains: 4013* this study n = 2, USA n = 1.

** Lineage designations according to SITVIT2 using revised SpolDB4 rules; “Unknown” designates patterns with signatures that do not belong to any of the major lineages described in the database.

*** Clustered strains correspond to a similar spoligotype pattern shared by 2 or more strains “within this study”; as opposed to unique strains harboring a spoligotype pattern that does not match with another strain from this study. Unique strains matching a preexisting pattern in the SITVIT2 database are classified as SITs, whereas in case of no match, they are designated as “orphan”.

Description of 40 shared-types (SITs; n = 87 isolates) and corresponding spoligotyping defined lineages/sublineages starting from a total of 103 M. tuberculosis strains isolated in Santiago, Chile.