Demographic data for cases of TBM and pulmonary tuberculosis recruited to the study.

a<p>Defined as the main place of residence on entry to the study. Urban addresses were those within the central districts of Ho Chi Minh City (HCMC); sub-urban addresses were those within the outer districts of HCMC; rural (HCMC surrounds) addresses were in the immediate surrounding rural districts of HCMC; the other rural addresses were defined by whether they were south east or south west of HCMC.</p

<i>TLR</i>2 T597C SNP allele and bacterial genotype frequencies: comparison with host genotype distribution in the cord blood control group.

a<p>OR was calculated comparing each group to the genotype/allele distribution in the cord blood controls.</p

<i>Mycobacterium tuberculosis</i> lineages defined by large sequence polymorphism (LSP) analysis.

<p>The circles represent Region of difference (RD region) deleted in each lineage. Only East Asian, Indo-Oceanic and Euro-American lineages were identified in Vietnam.</p

LSP lineages of <i>M. tuberculosis</i> isolates causing pulmonary and meningeal tuberculosis.

a<p>Undefined isolates failed to generate a product on repeated PCR for one of the two RD regions despite generating product for other PCRs; it is likely these isolates carried additional deletions or mutations in the primer region.</p>b<p>Odds ratio was calculated comparing the meningeal and pulmonary proportions for each lineage.</p

Spoligotype, IS6110 RFLP and MIRU typing for all <i>M. tuberculosis</i> isolates in the study.

a<p> where <i>N</i> = the total number of strains in the sample population, <i>s</i> = the total number of types described and <i>n_j</i> = the total number of strains belonging to the <i>j</i>^th type <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Hunter1" target="_blank">[52]</a>.</p>b<p>ST319, also known as the Vietnam genotype <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Anh1" target="_blank">[39]</a>.</p>c<p>The Ha Noi genotype has a single IS6110 copy and is prevalent throughout Vietnam <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Le1" target="_blank">[53]</a>.</p>d<p><i>M. tuberculosis</i> isolates with no IS6110 insertion elements are relatively common in South-East Asia and have been reported in several studies of Vietnamese strains <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Le1" target="_blank">[53]</a>,<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Yuen1" target="_blank">[54]</a>.</p>*<p>Isolates of East-Asian Genotype in the LSP typing system of Gagneux et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Gagneux1" target="_blank">[24]</a>.</p>†<p>Isolates of the Indo-Oceanic genotype in the LSP typing scheme of Gagneux et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000034#ppat.1000034-Gagneux1" target="_blank">[24]</a>.</p