P74
Analysis of genomic variants outside the drug-resistant zones – understanding other mutations and their consequences
M Grobbelaar(1) H Cox(1) R M Warren(1) E M Streicher(1) A Dippenaar(1)
1:University
Background:
Genomic variants linked to drug resistance and fitness have been widely studied using patient isolates. However limited studies have focused on other variants and their influence on virulence, bacterial fitness, transmission, and drug tolerance.
Methods:
We investigated 49 DR-TB cases with multiple isolates in a large retrospective cohort study in a high TB-incidence setting in Cape Town, South Africa. DNA was extracted using the CTAB and standard phenol/chloroform extraction methods.
WGS was performed using the Illumina NextSeq 550 platform, the Illumina HiSeq2500 platform, and the Illumina NovaSeq 6000 platform. Sequencing libraries were prepared using the NEBNext_Ultra_II_FS_DNA library preparation kit and the NexteraXT library preparation kit as per the manufacturer's instructions.
Sequences were analyzed with a customized pipeline as previously described using open-source software. Drug resistance-conferring and associated mutations were identified using TB-Profiler.
Results:
The majority of non-drug resistant variants belonged to cell wall and cell processes (31.09%), conserved hypothetical (23.75%), intermediary metabolism and respiration (19.35%) and information pathway (7.33%). While 28.87% of variants were found in the intergenic regions, 2.93% esxV, 2.09% Rv3169, 1.67% Rv3758c and 1.46% esxP and Rv0758 respectively.
Discussion:
Genomic studies usually focus on the drug resistance-causing genes and a lot of information is wasted by not assessing other minor variants. The most common variants were in intergenic regions which have been found to express signals in microarray studies. Little is known about how these intergenic regions can affect drug resistance.
Conclusion:
Similar genes were identified in multiple unrelated patients treated for drug-resistant tuberculosis.