Whole-genome sequencing data of Corynebacterium diphtheriae isolated from diphtheria outbreaks in Indonesia.

() is the causative agent of diphtheria. The main virulence factor of is diphtheria toxin, which is encoded by the gene and regulated by the gene. The and genes are used as genetic markers to identify bacteria causing diphtheria by PCR. Here, we present the whole-genome sequencing (WGS) data of 18  isolates from diphtheria outbreaks in different regions in Indonesia. We used these data to identify (SNPs) associated with the and genes to verify the accuracy of the PCR assay and performed molecular typing with a multilocus sequence typing (MLST) approach. The data can be used for further analyses, such as antimicrobial resistance and bacterial virulence factors.