Comparison of Molecular and Phenotypic Methods for the Detection and Characterization of Carbapenem Resistant Enterobacteriaceae

Abstract

In recent years, there has been a rapid dissemination of carbapenem resistant Enterobacteriaceae (CRE). This study aimed to compare phenotypic and molecular methods for detection and characterization of CRE isolates at a large tertiary care hospital in Saudi Arabia. This study was carried out between January 2011 and November 2013 at the King Khalid University Hospital (KKUH) in Saudi Arabia. Determination of presence of extended-spectrum beta-lactamases (ESBL) and carbapenem resistance was in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. Phenotypic classification was done by the MASTDISCSTM ID inhibitor combination disk method. Genotypic characterization of ESBL and carbapenemase genes was performed by the Check-MDR CT102. Diversilab rep-PCR was used for the determination of clonal relationship. Of the 883 ESBL-positive Enterobacteriaceae detected during the study period, 14 (1.6%) isolates were carbapenem resistant. Both the molecular genotypic characterization and phenotypic testing were in agreement in the detection of all 8 metalo-beta-lactamases (MBL) producing isolates. Of these 8 MBL-producers, 5 were positive for blaNDM gene and 3 were positive for blaVIM gene. Molecular method identified additional blaOXA gene isolates while MASTDISCSTM ID detected one AmpC producer isolate. Both methods agreed in identifying 2 carbapenem resistant isolates which were negative for carbapenemase genes. Diversilab rep-PCR analysis of the 9 Klebsiella pneumoniae isolates revealed polyclonal distribution into eight clusters. MASTDISCSTM ID is a reliable simple cheap phenotypic method for detection of majority of carbapenemase genes with the exception of the blaOXA gene. We recommend to use such method in the clinical laboratory.

Emergence of armA and rmtB genes among VIM, NDM, and IMP metallo-β-lactamase-producing multidrug-resistant Gram-negative pathogens

“…Among the ESBLs, CTX-M was the most common gene found (16.5%) both individually and in combination (22.3%), followed by TEM-type ESBLs (9.7%) individually and (15.5%) in association and SHV-type ESBLs (4.8%) individually and (1.9%) in association. PCR for MBLs showed bla NDM-1 and bla VIM (6.7%) to be the most dominant type found followed by bla IMP (3.8%) and bla SIM-1 (0.9%) gene similar to a study by Somily et al [34]. One E. coli strain was found to harbor SIM-1 gene and another E. coli strain, which was identified with high resistance to all the antibiotics except colistin was positive for bla CTX-M , bla TEM , bla NDM-1 , armA, and rmtB genes.…”

Emergence of NDM-1 among carbapenem-resistant Klebsiella pneumoniae in Iraqi hospitals

“…A recent study from Turkey tested 77 isolates of K. pneumoniae and found that 74 isolates (89.16%) produced OXA-48 carbapenemase, whereas nine isolates (10.84%) produced both OXA-48 and NDM-1 by both phenotypic tests included CarbaNP test and CIM test [29]. Genotypic characterization of ESBL and carbapenemase genes by the Check-MDR CT102 was fully in agreement with phenotypic testing in the detection of 8 MBL in study by Somily et al [30].…”

Plasmid-mediated quinolone resistance among extended spectrum beta lactase producing Enterobacteriaceae from bloodstream infections

“…For the optimal detection of carbapenem-resistant microorganisms, molecular biological methods are recommended. However, in resource-limited settings, a combination of phenotypic tests can be applied in diagnostic labs [36].…”