Evaluation of the SpeeDx Carba (beta) multiplex real-time PCR assay for detection of NDM, KPC, OXA-48-like, IMP-4-like and VIM carbapenemase genes
BMC Infectious Diseases
Bordin A1, Trembizki E1, Windsor M2, Wee R2, Tan LY2, Buckley C1, Syrmis M1,3, Bergh H3, Cottrell K1, Zowawi HM1,4,5,6,7, Sidjabat HE1, Harris PNA1,3, Nimmo GR3,8, Paterson DL1, Whiley DM9,10.
1 The University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia.
2 SpeeDx Pty. Ltd., Brisbane, Queensland, Australia.
3 Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia.
4 College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
5 World Health Organization Collaborating Centre for Infection Prevention and Control, Riyadh, Saudi Arabia.
6 Gulf Cooperation Council Center for Infection Control, Riyadh, Saudi Arabia.
7 King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia.
8 Griffith University School of Medicine, Brisbane, Queensland, Australia.
9 The University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia. firstname.lastname@example.org.
10 Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia. email@example.com.
Year of Publication:
Carbapenemase-producing organisms (CPOs) have emerged as antibiotic-resistant bacteria of global concern. Here we assessed the performance of the Carba (beta) assay, a multiplex real-time PCR assay developed by SpeeDx for the detection of key carbapenemase-encoding genes: KPC, NDM, OXA-48-like, IMP-4-like, and VIM.
DNA extracts of 180 isolates were tested with the Carba (beta) assay, using previously validated in-house TaqMan probe assays for the relevant carbapenemase genes as the reference standard. The Carba (beta) assay was then directly used to screen 460 DNA extracts of faecal specimens, with positive results subjected to the aforementioned in-house assays plus Sanger sequencing.
The Carba (beta) assay correctly identified the presence of the respective carbapenemase genes in 154 of 156 isolates and provided negative results for all 24 non-CPO isolates. Two isolates provided positive results for OXA-48-like carbapenemase by the Carba (beta) assay only. The Carba (beta) assay had sensitivities of 100% for all targets, and specificities of 100% for KPC, NDM, IMP-4-like, and VIM targets, and 98.5% for OXA-48-like targets. When applied directly to faecal specimens, eight samples were positive by the Carba (beta) assay, two of which were confirmed by in-house TaqMan probe PCR or DNA sequencing.
The Carba (beta) assay is highly sensitive and specific for detecting key carbapenemase genes in isolates. Further testing is required to assess this assay’s suitability for direct screening of clinical specimens.