Mycobacterium tuberculosis DNA detection in formalin-fixed paraffin-embedded tissue using Digital PCR: a proof-of-concept study

Abstract

This proof-of-concept study aimed to assess whether digital PCR (dPCR) technology could improve the detection of M. tuberculosis complex (MTB) from formalin-fixed paraffin-embedded (FFPE) tissue when compared to real-time PCR. A laboratory developed test using real-time PCR assay targeting the MTB-IS6110 was transitioned to dPCR technology. The analytical sensitivity of dPCR using strain H37Rv genomic DNA was 2.5 fg/reaction, which was lower than the 5 fg/reaction detected by real-time PCR. Archived DNA from 72 samples were evaluated retrospectively and compared to real-time PCR. The dPCR demonstrated 100 % (33/33) PPA and 94.7 % (38/39) NPA with real-time PCR. Thirteen samples with results near the limit of detection by real-time PCR were also at the limit of detection by dPCR. This study demonstrated that, while dPCR provided high analytical sensitivity, its performance for the MTB detection in FFPE tissues was comparable to that of real-time PCR. Both dPCR and real-time PCR are valuable tools for MTB detection especially in the absence of mycobacterial culture.