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Background  Tuberculosis (TB) is caused by a bacterium called  Mycobacterium tuberculosis  (Mtb). China is the third in top 8 high TB burden countries and Guangxi is one of the high incidence areas in South China. Determine bacterial factors that affected TB incidence rate is a step toward Ending the TB epidemic.    Results  Genomes of  M. tuberculosis  cultures from a relatively high and low incidence region in Guangxi have been sequenced. 347 of 358(96.9%) were identified as  M. tuberculosis . All the strains belong to Lineage 2 and Lineage 4, except for one in Lineage 1. We found that the genetic structure of the  M. tuberculosis  population in each county varies enormously. Low incidence rate regions have a lower prevalence of Beijing genotypes than other regions. Four isolates which harbored  mutT4 -48 also had  mutT2 -58 mutations. It is suggested that strains from the ancestors of modern Beijing lineage is circulating in Guangxi. Strains of modern Beijing lineage (OR=2.04) were more likely to acquire drug resistances than Lineage 4. Most of the lineage differentiation SNPs are related to cell wall biosynthetic pathways.    Conclusions  These results provided a higher resolution to better understand the history of transmission of  M. tuberculosis  from/to South China. And the incidence rate of tuberculosis might be affected by bacterial population structure shaped by demographic history. Our findings also support the hypothesis that Modern Beijing lineage originated in South China.

A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China