A total of 133 MDR-MTB clinical isolates were collected from Chongqing from November 2014 to February 2016. PZA susceptibility was determined by BACTEC MGIT 960 TB system. The pncA and rpsA genes were amplified by PCR and the products were analyzed by DNA sequencing in order to identify the mutations in pncA and rpsA genes and the correlations with PZA resistance.

Among the 133 MDR-TB clinical strains, 83 isolates were resistant to PZA, yielding a resistance rate of 62.4%. Sequence analysis revealed that 73 out of 83 (87.9%) MDR-MTB strains harbored a mutation located in the pncA gene. Four out of 50 (8.0%) PZA-sensitive isolates occurred pncA gene mutation. The PZA-resistant strains showed higher mutation rate than the PZA-sensitive strains (χ ²=81.82, P=0.000). Most of the pncA gene mutations in the genomes of PZA-resistant strains were base substitution mutation, especially the G395A substitution (9 isolates). The identified mutations were dispersed along the pncA gene, distributing in the region from nucleotide -11 to nucleotide 515. The pncA gene mutations centralized in the regions of 20-40, 136-146, 185-226, and 392-408. Eighteen novel mutation sites of pncA gene were observed including T2C, T37G, T94G, C206T, G319A, C437T, T488C, GCC insertion at 52, C insertion at 130, CA insertion at 139, C insertion at 232, T insertion at 243, A insertion at 288, GGT insertion at 393, CA insertion at 408, ACGCC deletion at 341, GCCAC deletion at 342, and GATGAGGTC deletion at 376. The pncA gene mutations in the genomes of PZA-sensitive strains were only the substitution mutations, and the sites were different from those of PZA-resistant strains. While no genetic mutation associated with PZA resistance was found in the rpsA gene.

The MDR-MTB strains showed higher resistance rate to PZA in Chongqing. Mutation in pncA gene might be one of the major mechanisms of resistance to PZA in MDR-MTB isolates in Chongqing.