This nationwide study funded by the Swiss National Science Foundation aims to analyse differences in the genetic population structure of Mycobacterium tuberculosis and the associations between the genetic M. tuberculosis strain variation, patient’s origin and disease manifestations in HIV co-infected compared to HIV-negative tuberculosis (TB) patients diagnosed between 2000 and 2008.  It combines collection of clinical information from patient and molecular investigations of the M. tuberculosis strains causing the disease.

Specifically, we will pursue the following objectives:

• To analyze the genetic diversity of M. tuberculosis strains; and to analyze the distribution and epidemiological clustering of “allopatric” versus “sympatric” lineages;
• To analyze the distribution and epidemiological clustering of mutations conferring resistance to first-line antibiotics (isoniazide, rifampicin and ethambutol); and to analyze the association of particular mutations with M. tuberculosis lineages (genetic background);
• To study the relationship between particular M. tuberculosis genotype (defined by bacterial lineage, SNP-haplotype, drug resistance genotype) and clinical characteristics.