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

Abstract

<p style="text-align: justify;"><strong>Aim</strong> <br />To compare the sequences of the <em>tcd</em>C gene between Clostridioides difficile (C. <em>difficile</em>) strains identified as PCR ribotype 176 and the reference strain C. <em>difficile</em> PCR ribotype 027 and to evaluate the use of the Xpert C. <em>difficile</em>/Epi assay for their differentiation. <br /><strong>Methods</strong> <br />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). <br /><strong>Results</strong> <br />Four strains (out of seven; 57%) characterized as PCR ribotype 176 had 100% identity of the <em>tcd</em>C gene with the reference strain. The average length of the <em>tcd</em>C 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 <em>tcd</em>C 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. <br /><strong>Conclusion</strong> <br />PCR ribotype 176 strains have almost the same <em>tcd</em>C gene sequence as PCR ribotype 027, resulting in misidentification of this PCR ribotype by the Xpert C. <em>difficile</em>/Epi assay. Information about presumptive positive results based on deletion in the tcdC gene should be treated with caution or disregarded.</p>