Toxin gene truncation via IS1132 in non-toxigenic toxin gene-bearing (NTTB) Corynebacterium diphtheriae

Recently a Corynebacterium diphtheriae (C. diphtheriae) outbreak was reported in Europe described as the largest upsurge of cases in the last 70 years. Clinically relevant infections and transmission events are not necessarily associated only with toxigenic strains, but they can also be caused by non-toxigenic diphtheria toxin gene-bearing (NTTB) C. diphtheriae. PCR-based identification of potentially toxigenic strains needs to be complemented by testing for diphtheria toxin (DT) production, which is why diagnosis is notoriously difficult.

C. diphtheriae was cultivated from an intraoperative swab. The strain although PCR positive for tox gene, lacked DT expression in Elek test and was thus categorized as non-toxigenic tox-bearing (NTTB). Short- and long-read whole-genome sequencing (WGS) revealed a truncated tox gene. At nucleotide position 19, the insertion sequence IS1132 was inserted in the reverse direction. The isolate had a novel sequence type, ST-1111, and core genome MLST (cgST-3956 in BIGSdb-Pasteur's nomenclature) showed it is not related to any of the previously described C. diphtheriae outbreak strains in Germany.

Here we report a novel ST of NTTB C. diphtheriae with interruption of its tox gene by IS1132 at nucleotide position 19. Our findings highlight the value of WGS for resolving potentially toxin-positive cases and for reliably assessing the clinical risk and epidemiological context, which are the key prerequisites for infection control measures and public health responses.