Analysis on mutations in the genes of ESX-4 secretion system of Mycobacterium tuberculosis isolated from Southern Xinjiang

Objective To compare the mutation differences of the virulence genes of ESX-4 system in clinical isolates of Mycobacterium tuberculosis in different lineages and with different drug resistance, and explore the polymorphisms of ESX-4 system gene in clinical isolates.

Methods Whole-genome sequencing was performed on 807 M. tuberculosis clinical isolates in southern Xinjiang. The mutation profiles of the ESX-4 system virulence genes as well as the lineages and drug susceptibility results were detected using TB-profiler software and C++ Script program. Descriptive analysis method, the χ² test and logistics regression model were performed on the data.

Results A total of 119 single nucleotide polymorphic sites and 12 different insertions/deletions were found in 807 M. tuberculosis isolates. The genes with top three non-synonymous mutation rates were Rv3446c (43.12%), esxU (40.02%), and eccC4 both eccD4 genes (both 23.30%). Lineage 2(L2) isolates accounted for 62.70% (506/807), L3 isolates accounted for 19.45% (157/807) and L4 isolates were 17.84% (144/807). In addition, the susceptible isolates accounted for 39.41% (318/807), drug-resistant isolates accounted for 60.59% (489/807); and the rifampicin resistant rate was 34.08% (275/807), isoniazid resistant rate was 28.50% (230/807), quinolones resistant rate was 12.14% (98/807). The mutation rates of both eccC4 and esxT genes were significantly higher in the L3 isolates than in L2 or L4 isolates. Multivariate logistic regression model analysis revealed that L2 and isoniazid resistance were risk factors for mutations in esxU and Rv3446c genes (all OR>1, all P<0.001), and MDR was an additional risk factor for Rv3446c mutation (OR=1.94, 95%CI: 1.12–3.37).

Conclusion Our results identified gene mutations associated with L2、L3 isolates and drug resistance in the ESX-4 secretion system of M. tuberculosis, which provided basic scientific evidence for further research on the transmission, drug resistance and pathogenic mechanism of M. tuberculosis.