Combined selective culture and molecular methods for the detection of carbapenem-resistant organisms from fecal specimens

Rebecca Yee, Stefanie Fisher, Yehudit Bergman, Krizia K. Chambers, Pranita D. Tamma, Karen C. Carroll, Patricia J. Simner*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Detection of patients with intestinal colonization of carbapenem-resistant organisms (CRO), or more specifically carbapenemase-producing (CP) CRO, can prevent their transmission in healthcare facilities and aid with outbreak investigations. The objective of this work was to further develop and compare methods that combine selective culture and/or PCR to rapidly detect and recover CRO from fecal specimens. Molecularly characterized Gram-negative bacilli (n = 62) were used to spike fecal samples to establish limit of detection (LOD; n = 12), sensitivity (n = 28), and specificity (n= 21) for 3 methods to detect CP-CRO: direct MacConkey (MAC) plate and Xpert Carba-R (Cepheid) on growth, MAC broth and Carba-R testing of the broth, and direct testing by Carba-R. This was followed by a clinical study comparing methods in parallel for 286 fecal specimens. The LOD ranged from 102-105 CFU/mL depending on the carbapenemase gene and method. Combined culture/PCR methods had a sensitivity of 100%, whereas direct Carba-R testing had a sensitivity of 96% for the detection of CP-CRO. All methods had specificities of 100%. The prevalence of CP-CRO (0.7%) and non-CP-CRO (5.2 %) were low in the clinical study, where all methods demonstrated 100% agreement. The three methods performed comparably in detecting CP-CRO. Direct Carba-R testing had a higher LOD than the combined selective culture methods, but this may be offset by its rapid turnaround time for detection of CP-CRO. The selective culture methods provide the benefit of simultaneously isolating CP-CRO in culture for follow-up testing and detecting non-CP-CRO.

Original languageAmerican English
Pages (from-to)2315-2321
Number of pages7
JournalEuropean Journal of Clinical Microbiology and Infectious Diseases
Issue number11
StatePublished - Nov 2021
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.


  • Carbapenem-resistant organisms
  • Carbapenemase
  • Methods
  • Public health
  • Surveillance


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