In order to provide a global overview of genotypic, epidemiologic, demographic, phylogeographical,
and drug resistance characteristics related to the prevailing tuberculosis (TB) epidemic,
we hereby report an update of the 6th version of the international genotyping database
SITVIT2. We also make all the available information accessible through a dedicated
website (available at http://www.pasteur-guadeloupe.fr:8081/SITVIT2). Thanks to the
public release of SITVIT2 which is currently the largest international multimarker
genotyping database with a compilation of 111,635 clinical isolates from 169 countries
of patient origin (131 countries of isolation, representing 1032 cities), our major
aim is to highlight macro- and micro-geographical cleavages and phylogeographical
specificities of circulating Mycobacterium tuberculosis complex (MTBC) clones worldwide.
For this purpose, we retained strains typed by the most commonly used PCR-based methodology
for TB genotyping, i.e., spoligotyping based on the polymorphism of the direct repeat
(DR) locus, 5-loci Exact Tandem Repeats (ETRs), and MIRU-VNTR minisatellites used
in 12-, 15-, or 24-loci formats. We describe the SITVIT2 database and integrated online
applications that permit to interrogate the database using easy drop-down menus to
draw maps, graphics and tables versus a long list of parameters and variables available
for individual clinical isolates (year and place of isolation, origin, sex, and age
of patient, drug-resistance, etc.). Available tools further allow to generate phylogenetical
snapshot of circulating strains as Lineage-specific WebLogos, as well as minimum spanning
trees of their genotypes in conjunction with their geographical distribution, drug-resistance,
demographic, and epidemiologic characteristics instantaneously; whereas online statistical
analyses let a user to pinpoint phylogeographical specificities of circulating MTBC
lineages and conclude on actual demographic trends. Available associated information
on gender (n = 18,944), age (n = 16,968), drug resistance (n = 19,606), and HIV serology
(n = 2673), allowed to draw some important conclusions on TB geo-epidemiology; e.g.
a positive correlation exists between certain Mycobacterium tuberculosis lineages
(such as CAS and Beijing) and drug resistance (p-value<.001), while other lineages
(such as LAM, X, and BOV) are more frequently associated with HIV-positive serology
(p-value<.001). Besides, availability of information on the year of isolation of strains
(range 1759-2012), also allowed to make tentative correlations between drug resistance
information and lineages - portraying probable evolution trends over time and space.
To conclude, the present approach of geographical mapping of predominant clinical
isolates of tubercle bacilli causing the bulk of the disease both at country and regional
level in conjunction with epidemiologic and demographic characteristics allows to
shed new light on TB geo-epidemiology in relation with the continued waves of peopling
and human migration.