ABSTRACT
The purpose of this investigation was to compare the performance of species-specific polymerase chain reaction (PCR), matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and phenotypic identification systems for the identification of Enterococcus species. A total of 132 clinical isolates were investigated by the following: (1) a multiplex real-time PCR assay targeting ddl Enterococcus faecium, ddl Enterococcus faecalis, vanC1 and vanC2/C3 genes, and a high-resolution melting (HRM) analysis of the groESL gene for the differentiation of Enterococcus casseliflavus and Enterococcus gallinarum; (2) Bruker MS; (3) VITEK MS; and (4) the VITEK 2 system. 16S rRNA gene sequencing was used as a reference method in the study. The 132 isolates were identified as 32 E. faecalis, 63 E. faecium, 16 E. casseliflavus and 21 E. gallinarum. The multiplex PCR, Bruker MS and VITEK MS were able to identify all the isolates correctly at the species level. The VITEK 2 system could identify 131/132 (99.2 %) and 121/132 (91.7 %) of the isolates at the genus and species levels, respectively. The HRM-groESL assay identified all (21/21) E. gallinarum isolates and 81.3 % (13/16) of the E. casseliflavus isolates. The PCR methods described in the present study are effective in identifying the enterococcal species. MALDI-TOF MS is a rapid, reliable and cost-effective identification technique for enterococci. The VITEK 2 system is less efficient at detecting non-faecalis and non-faecium Enterococcus species.
Subject(s)
Bacterial Typing Techniques/methods , Bacteriological Techniques/methods , Enterococcus/classification , Enterococcus/isolation & purification , Gram-Positive Bacterial Infections/diagnosis , Polymerase Chain Reaction/methods , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Bacterial Typing Techniques/economics , Bacteriological Techniques/economics , Costs and Cost Analysis , Enterococcus/chemistry , Enterococcus/genetics , Humans , Polymerase Chain Reaction/economics , Sensitivity and Specificity , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/economicsABSTRACT
A laboratory-developed test (Lab Assay), combining enrichment broth and real-time polymerase chain reaction (PCR) for vancomycin-resistant enterococci (VRE) screening, was developed and evaluated in this study. A total of 1,765 faecal or rectal swabs sent to the laboratory for VRE screening were investigated in parallel by Lab Assay and the Roche LightCycler VRE detection kit-based method. The diagnostic values for Lab Assay were as follows: 100% sensitivity, 79.92% specificity, 1.94% positive predictive value and 100% negative predictive value, which were comparable to the results from the LightCycler kit-based assay. The detection limit of Lab Assay was 10(0) to 10(1) colony-forming units (CFU)/ml of inoculum in broth for both VanA-type and VanB-type VRE. The PCR method developed in this study was approved to be applicable on both the Applied Biosystems 7500 Fast Real-Time PCR System and the LightCycler(®) 480 Real-Time PCR System. The flexibility in choosing PCR systems makes it possible that the PCR assay could be fully compatible with the DNA extraction's platform, providing an integrated workflow. Furthermore, the material cost is saved at 7EUR per sample when Lab Assay replaces the commercial kit-based method in our routine screening for VRE. Therefore, the laboratory-developed broth-PCR method is an efficient and economical assay for VRE screening.
