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

Abstract

Background: The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database.

Results: The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network.

Conclusion: Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

Figure 1

Bioinformatical (62 lineages/sub lineages prototype patterns) and statistical (50 most frequent) classification analysis of SpolDB4. First column ST n°: Shared-type (ST) number of prototype pattern for the linage/sub lineage. Second column: lineage/sub lineage name. Third column: Binary spoligo display with black-white squares for respectively hybridizing-non-hybridizing spacers. Fourth column: Octal code (in red: defining octal rule). Fifth column: total absolute number of isolates of the subclass when variant ST spoligos are included (using SpolNet). Sixth column: same but expressed as percentage of total clustered isolates. * Total number and Frequency for these types are already included in their mother clade if known. Undesignated types are counted within the T1-ill-defined lineage. ** in red: octal rule defining the genotype.

Figure 2

Percentage of main spoligotyping-defined MTC genotype families within SpolDB4 (Beijing, Beijing-like, CAS, EAI, Haarlem, LAM, Manu, X, T), by studied continents and worldwide. Abbreviations : AFR = Africa, CAM = Central America, EUR = Europe, FEA = Far-East Asia, MECA = Middle-East and Central Asia, NAM = North America, OCE = Oceania, SAM = South America.

Figure 3

Synthesizing World Maps showing absolute (diameter) and percentage (colour) numbers of 3 genotype families within each country: Beijing; EAI (East-African Indian) CAS (Central Asia). These maps were built on an updated SpolDB4 on 2005 September 14^th, on clusters of the 50 most frequent shared types as shown in Table 1, for a total of n = 17212 isolates (Beijing n = 4042, EAI n = 1684, CAS n = 1022).

Figure 4

Synthesizing World Maps showing absolute (diameter) and percentage (colour) numbers of 3 genotype families within each country: M. bovis; Haarlem; Latin-American and Mediterranean (LAM). These maps were built on an updated SpolDB4 on 2005 September 14^th, on clusters of the 50 most frequent shared types as shown in figure 1, for a total of n = 17212 isolates (M. bovis n = 3888, LAM n = 3400, Haarlem n = 3176). Maps were built using Philcarto (P. Waniez, version 4.38).