Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Abstract

Aim To compare the sequences of the tcdC gene between Clostridioides difficile (C. difficile) strains identified as PCR ribotype 176 and the reference strain C. difficile PCR ribotype 027 and to evaluate the use of the Xpert C. difficile/Epi assay for their differentiation. Methods A total of 45 strains were grown from storage beads. DNA of sufficient quality and quantity for sequencing was extracted from 9 samples. Single consensus sequences of PCR ribotype 176 strains and PCR ribotype 001, PCR ribotype 070 (a control group) were mapped to a reference genome of strain CDI-01 (PCR ribotype 027). Results Four strains (out of seven; 57%) characterized as PCR ribotype 176 had 100% identity of the tcdC gene with the reference strain. The average length of the tcdC gene in these four strains (PCR ribotype 176) was 643 bp, which is 36 bp shorter than the reference genome. Three strains (PCR ribotype 176) had a percentage identity of the tcdC gene in the range of 99.37-100%. Strains 25 (PCR ribotype 001) and 28 (PCR ribotype 070) had a similarity in the range of 95.39-95.63% as a result of different ribotype to the reference strain. Conclusion PCR ribotype 176 strains have almost the same tcdC gene sequence as PCR ribotype 027, resulting in misidentification of this PCR ribotype by the Xpert C. difficile/Epi assay. Information about presumptive positive results based on deletion in the tcdC gene should be treated with caution or disregarded.

Keywords

• DNA
• mutation
• polymerase chain reaction