Abstract
Corynebacterium diphtheriae (C. diphtheriae) is the causative agent of diphtheria. The main virulence factor of C. diphtheriae is diphtheria toxin, which is encoded by the tox gene and regulated by the dtxR gene. The tox and dtxR genes are used as genetic markers to identify bacteria causing diphtheria by PCR. Here, we present the whole-genome sequencing (WGS) data of 18 C. diphtheriae isolates from diphtheria outbreaks in different regions in Indonesia. We used these data to identify single nucleotide polymorphisms (SNPs) associated with the tox and dtxR 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.