The specific assays used to detect the presence of known carbapenemase genes is located on plasmids or efflux pump mutations are normally gene based and amplify the potential genes present by the use of oligomer primers and probes.
Screening for CRE colonization is usually based on microbiological evaluation of the rectal swabs. Nasal swabs, pharyngeal swab, bronchial aspirates , urine cultures in catherized patients should be carefully evaluated. The rectal swab helps in detection to view the presence of intestinal CRE. The following are the surveillance test used to detect CRE :
1. culture-based methods;
2. nucleic acid amplification technology (NAAT)-based assays.
Culture based method for CRE screening:
Culture based methods have been widely used for CRE screening, several different cultural approaches have been described
a) inoculation onto McConkey agar plate after broth enrichment
b) direct inoculation onto McConkey agar plate containing a meropenem disk
c) direct inoculation onto specific selective chromogenic media
but the above protocol is time consuming and it might take atleast 48-72 hours.
The main advantage of direct inoculation onto the McConkey agar plate containing a meropenem disk include low cost, and evaluation of the suspected colonies and also the possibility of checking the quality of the samples.
NAAT for molecular screening:
Molecular based methods (NAAT) for CRE screening usually detect the presence of one or more carbapenemase genes. For these characteristics these assays are able to identify only previously known resistance determinants.
NAAT-based assays validated for carbapenemase genes detection from rectal swabs can also be used as a confirmatory test for suspected colonies identified by culture-based methods, although not all commercial assays have an on-label indication for this.
The three types of NAAT based assays for the Surveillance of CRE is as follows:
In house molecular methods
Commercial molecular assays
Rapid/easy to use commercial molecular assays:
In house molecular methods can reveal best level of sensitivity and specificity . Moreover, these assays are less expensive if compared to molecular commercial method. Also it has important disadvantages are low level of automation, standardization and validation, and suboptimal inter-laboratory reproducibility.
Commercial molecular assays:
they are highly sensitive, specific and standardized, with TAT of few hours; the level of automation of these methods can vary from poor (need of sample preparation step, including extraction or lysis, and/or multiple hands-on steps), to good, but for all these assays laboratory experience and equipment are required.
Rapid/easy to use commercial molecular assays (REU-CMA) :
They might provide the same high standard of quality of results with shorter hands-on time and TAT (less than 1 h) and no requirement for batching