Evaluation of two commercial real-time PCR assays for detection of carbapenemase genes in Enterobacteriaceae

Development and Validation of a Multiplex Real-Time PCR Assay for Rapid Screening of Main Carbapenemase Genes in Clinical Isolates and Surveillance Samples

BACKGROUND/OBJECTIVES

Carbapenem-resistant Enterobacterales, largely due to carbapenemase production, are significant public health threats, which compromise treatment with key β-lactam antibiotics. Early detection is essential for guiding therapy and controlling spread. This study describes the design, optimisation and validation of a multiplex real-time PCR for the screening of the most frequent carbapenemases in our area.

METHODS

Primers and probes targeted at genes encoding carbapenemases blaKPC, blaIMP, blaVIM, blaNDM and blaOXA-48-group were designed and adapted for the development, and in silico and experimental validation of a single-tube real-time PCR.

RESULTS

A good linear correlation between the fluorescence values in the real-time PCR and the log10 of bacterial concentration of each carbapenemase-containing bacterial suspension was observed (R2 > 0.98). The limit of detection was 2-15, 16-256, 42-184, 4-42, 42-226 CFU/reaction of VIM-, IMP-, NDM-, KPC- and OXA-48-carbapenemase-containing bacteria, respectively. Intra-assay coefficient of variation for the mean Ct values ranged from 0.99% for OXA-48 to 3.34% for KPC. Inter-assay variability remained below 7%. Real-time PCR tested on bacterial isolates yielded 100% sensitivity and specificity. Analysis of rectal swabs using extracted DNA and a DNA extraction-free protocol showed good concordance with culture-based phenotypic methods. Additionally, the molecular method could detect all targets, except for one sample where only the DNA extraction-free protocol detected NDM.

CONCLUSIONS

The assay offers a rapid, sensitive and specific method for the screening of major carbapenemase genes, providing an effective tool for surveillance and infection control in clinical settings. The DNA extraction-free protocol converts this method into a good alternative for screening in 24/7 clinical laboratories. Further multiplexing to target other resistance genes, on demand, could add potential benefits to this laboratory-developed method.

Rapid Identification of Carbapenemase-producing Klebsiella pneumoniae strains by Matrix-Assisted Laser Desorption/Ionization-Time of Flight using Vitek® Mass Spectrometry System

Objective

The analysis of the protein pattern of Klebsiella pneumoniae carbapenemase (KPC)-producing strains by Bruker Matrix-Assisted Laser Desorption Ionization (MALDI) Biotyper system has revealed the presence, in the majority of cases, of an 11.109 m/z peak. The peak corresponds to the gene product named p019 of the bla _KPC-bearing plasmids and has been suggested as a candidate for a biomarker that is able to distinguish KPC-producers from non-KPC-producers. The aim of this study was to evaluate the rapid detection of the 11.109 m/z peak of KPC-producer strains in the clinical laboratory routine by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) technique, using the Vitek^® Research-User-Only (RUO) Mass Spectrometry (MS) system without changing the instrument parameters.

Materials and Methods

Globally, 373 K. pneumoniae isolates were investigated and identified by MALDI-TOF MS analysis. KPC-producers were distinguished from non-KPC-producers by Antimicrobial Susceptibility Testing (AST) and phenotypic carbapenemase resistance assays.

Results

The MALDI-TOF Vitek MS RUO detected the 11.109 m/z peak in 95.7% of KPC-producers with 100% specificity before traditional test results became available.

Conclusion

Our approach is appropriate as a first screening step for the rapid identification of KPC isolates, which will help to improve infection control in clinical practice and prevent the outbreak and dissemination of resistant bacteria.