Comparison of Clostridioides difficile nucleic acid amplification test (NAAT) results using fresh and frozen stool specimens and rectal swabs

Nucleic acid amplification tests (NAATs) are frequently used in Clostridioides difficile research and diagnostic testing, but the effect of freezing specimens on C. difficile NAAT performance is not well characterized. We compared C. difficile NAAT results between fresh and frozen fecal (n = 354) and rectal swab specimens (eSwab) (n = 132) using the Xpert system. Specimens were collected prospectively from 384 hospitalized patients admitted to the hematopoietic cell transplant and acute leukemia wards at a tertiary care hospital. Categorical concordance of NAAT results (agreement of positive/positive or negative/negative) was excellent between fresh and frozen conditions for fecal specimens (Kappa = 0.92) and very good for rectal swabs (Kappa = 0.78). Cycle threshold value correlation was similarly consistent between fresh and frozen conditions for swabs and stool specimens (Spearman’s correlation = 0.88). These results support the use of frozen fecal and rectal swab specimens to provide accurate results for research purposes when C. difficile NAAT testing on fresh specimens is not available or feasible.