Of 926 M. tuberculosis isolates with LSP/SNP-based lineage and spoligotyping information available, three cases were excluded because the identifiers were not unique, and four because the patients were infected by more than one strain of M. tuberculosis.
Based on the LSP/SNP from the 919 isolates, 481 (52.3%) belonged to the Euro-American lineage, 235 (25.6%) to the Indo-Oceanic lineage, 198 (21.5%) to the East-Asian lineage and 5 (0.5%) to the EAI lineage. Based on the spoligotype, 870 (95%) isolates belonged to a spoligotype family. The most frequent families were: EAI (n = 211, 23.0%), Beijing (n = 192, 20.9%) and T (n = 182, 19.8%); 49 isolates (5.3%) were not assigned to any family.
The relationship between the lineages and the families is shown in the . All the isolates belonging to each of the spoligotype families belonged to the same LSP/SNP-based lineage. Stated differently, the isolates from the Beijing family and those with a spoligotype in which all spacers are present belonged to the East-Asian lineage; the isolates from the T, Haarlem (H), X, Latin-American-Mediterranean (LAM) and S families belonged to the Euro-American lineage; the isolates from the EAI and MANU families to the Indo-Oceanic lineage; and the CAS family to the EAI lineage (). Because spoligotyping is used as a tool for molecular epidemiological studies, it will be possible to use the existing data to infer the main lineages of M. tuberculosis
in most of the cases. Such information could be important, given that different lineages of M. tuberculosis
have been suggested to have different clinical and epidemiological behaviors,4
and may impact the effectiveness of new diagnostics, drugs or vaccines.
Figure Description of the association of the three main LSP/ SNP lineages of M. tuberculosis in San Francisco and their respective spoligotype families. These families correspond to sub-lineages within the main LSP/SNP-based lineages. LSP = large sequence polymorphism; (more ...)
Of the 919 isolates, 141 (15%) had a unique spoligotype and 778 (85%) had a spoligotype that was identical to at least one other isolate. Among these 778 isolates, there were 76 different spoligotypes. All the isolates that had the same spoligotype belonged to the same lineage. Thus, we did not find any evidence of convergence of spoligotypes (κ = 1). The present analysis focused only on the main LSP/SNP-based lineages, however, and we did not test for convergence of spoligotypes within LSP/SNP-based sub-lineages. Thus, even though we were unable to detect convergence of spoligotypes among the main lineages of M. tuberculosis, it is still possible that this phenomenon occurs within individual LSP-based sub-lineages.
A further limitation of this study is that the collection of strains analysed is not representative of the global diversity of M. tuberculosis
, as we studied only three of the six main lineages.2
It is therefore possible that spoligotypes from any of the other three lineages (EAI, West-Africa I and II) may not be as informative or that their spoligotypes may be subject to convergent evolution.