A new phenotypic test, called the Carbapenem Inactivation Method (CIM), was developed to detect carbapenemase activity in Gram-negative rods within eight hours. This method showed high concordance with genotypic detection of carbapenemase encoding genes by PCR, and allows reliable detection of carbapenemase activity encoded by various genes in species of both Enterobacteriaceae and non-fermenters. Whole-genome sequencing analysis using Illumina HiSeq technology was applied to strains with an apparent discrepancy between genotypic and phenotypic detection of carbapenemase activity.