Evaluation of LAMP assay using phenotypic tests and PCR for detection of blaKPC gene among clinical samples

Carbapenem-resistant Enterobacteriaceae (CRE) infection constitutes a public health threat, which blaKPC was the major carbapenemases concerned in China. Timely and efficient diagnosis is of paramount importance for controlling the spread of drug-resistant bacteria. Here, we develop an approach based on loop-mediated isothermal amplification (LAMP) for rapid confirmation of blaKPC within 60 min from samples collected.

We designed primers specific to detect blaKPC and evaluated it for its sensitivity and specificity of detection using real-time monitoring. Five hundred forty-six clinical specimens were analyzed by the LAMP assay and compared with the phenotypic tests and PCR. The samples with inconsistent results were further verified by Sanger sequencing.

The LAMP assay displayed a detection limit of 1 × 10²  CFU/ml, which was 10-fold more sensitive than the PCR. No cross-reactivity was observed for strains that produced other types of β-lactamase. Furthermore, we demonstrated concordant results (Kappa > 0.75) between the genotypic method and phenotypic tests for the 546 clinical samples. The data presented in this study suggested that the genotypic method is a reliable assay for identifying blaKPC-induced CRE in China. The results of the Sanger sequencing indicate that the developed method not only has high accuracy but also meets the need for rapid diagnosis, while the PCR method is prone to false negatives.

We successfully constructed a LAMP technique that can be used for auxiliary diagnosis of CRE, which is faster, cheaper, and more accurate than the PCR. It may therefore be routinely applied for detection of blaKPC producers in routine clinical laboratories.