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Table 1 A. Definition of the variables (MC, Ar, SI) used in SpolDB4 to define : (1) the geographic index C1 (Endemic, Localized, Ubiquitous) (2) the quantitative index C2 (Epidemic, Common, Recurrent, Rare). B. Distribution of the 1939 Shared-types in 12 classes.

From: Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology

Name

Abbreviation

 

Type of data, Def.

Rules for Definition of Qualifiers (C1 and C2)

A Definitions

Matching Code

MC

 

1–8 digits, built by linking region codes

If 1 digit, then C1 = Endemic (genotype found in one macroregion only)

If 2 digits, then C1 = Localized (genotype found in two macroregions)

If ≥ 3 digits, go to Area section below for further interpretation

Area

Ar

 

numeric, n° of countries in which a given SIT is found

If MC ≥ 3 digits and Areas ≤ 5; C1 = Localized

If MC ≥ 3 digits and Areas ≥ 6; C1 = Ubiquitous (genotype found in more than three macroregions)

Spreading Index

SI

 

numeric, mean indicator of spreading independent of geography SI = n/Ar where n is the absolute value for a given shared-type

If SI ≥ 25; C2 = Epidemic

If 10 < SI < 24; C2 = Common

If 3 < SI < 9; C2 = Recurrent

If SI ≤ 2; C2 = Rare

B Distribution of the 1939 genotypes in 12 class

Endemic Epidemic

 

6

Endemic Recurrent

286

Localized Epidemic

 

2

Localized Recurrent

207

Ubiquitous Epidemic

 

6

Ubiquitous Recurrent

176

Endemic Common

 

31

Endemic Rare

501

Localized Common

 

14

Localized Rare

587

Ubiquitous Common

 

20

Ubiquitous Rare

82

NA*

 

21

Total

1939

*not applicable

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