Clinical Performance of Check-Direct CPE, a Multiplex PCR for Direct Detection of blaKPC, blaNDM and/or blaVIM, and blaOXA-48 from Perirectal Swabs

We evaluated the clinical performance of Check-Direct CPE for carbapenemase detection directly from 301 perirectal swabs (258 patients) in a nonoutbreak setting. Culture of a PCR-confirmed, carbapenemase-containing organism, or history of colonization with such organism within the previous 2 weeks, was used as the reference standard. Check-Direct CPE demonstrated a sensitivity value, specificity value, positive predictive value (PPV), and negative predictive value (NPV) of 100% (all bla(KPC)), 88%, 21%, and 100%, respectively. False positives accounted for 79% (n = 34) of samples for which a cycle threshold (C-T) value was reached. Simulated studies to evaluate specimen pooling as an approach to minimize costs showed no difference in C-T values for pooled groups of three or five that each contained a single specimen spiked with similar to 1,500 CFU bla(KPC) Klebsiella pneumoniae; however, the detection rate dropped to 60% at a seeded concentration of similar to 150 CFU. When data were pooled, C-T values for bla(KPC) were higher for heavy-feces-containing than for light-feces-containing liquid-suspended specimens. Furthermore, C-T values for liquid-suspended specimens were 4 to 5 C-T values lower (i.e., represented greater sensitivity) than those seen in direct swab analysis. Culture was equivalent to or better than Check-Direct CPE for 13/15 (87%) isolates tested in a limit-of-detection analysis. Detection of a carbapenemase gene at a C-T cutoff value of <= 35 was culture confirmed in 23/24 (96%) of cases; however, C-T values of >35 overlapped broadly between culture-positive (n = 21) and culture-negative (n = 36) specimens. Check-Direct CPE will likely prove most useful in high-prevalence areas or in outbreak settings where rapid carbapenemase detection is critical for infection control management.