Table 3.
Single and multiplex real-time PCRs used for the detection of the main antibiotic resistance genes in Enterobacteriaceae
| Approach | Detected resistance target | Nr. primers sets/probes | Cycling conditions | TTR (hrs) | Comments | Reference |
|---|---|---|---|---|---|---|
| Single real-time PCR | SHV (ESBLs variants) | 2 | 1 | 2 | SNPs are detected by the specificity of the primers | (Hammond, et al., 2005) |
| TEM (ESBLs variants) | 2/2 | 1 | 2 | SNPs are detected by the probes | (Mroczkowska & Barlow, 2008) | |
| CTX-M | 1/1 | 1 | 2 | Specific characterization | (Oxacelay, et al., 2009) | |
| CTX-M | 1/4 | 1 | 2 | Specific detection | (Birkett, et al., 2007) | |
| KPC | NA | 1 | 2 | Commercial kit (EasyQ KPC test, bioMerieux) | (Spanu, et al., 2012) | |
| KPC | 1/1 | 1 | <4 | Clinical implementation using enriched rectal swabs | (Singh, et al., 2012) | |
| KPC | 1/SG | 1 | 2 | Used previously published primers | (Raghunathan, et al., 2011) | |
| NDM-1 | 2/3 | 1 | 3 | Synthesized a positive control | (Kruttgen, et al., 2011) | |
| NDM-1 | 1/1 | 1 | 2 | Good performance of the TaqMan probe for copy number determination | (Manchanda, et al., 2011) | |
| NDM-1 | 1/1 | 1 | < 4 | From spiked stools | (Naas, Ergani, et al., 2011) | |
| OXA-48-like | 1/1 | 1 | < 4 | From spiked stools | (Naas, et al., 2013) | |
| CMY-2 | 1/SG | 1 | 2 | Quantification purpose | (Kurpiel & Hanson, 2011) | |
| OmpK35, OmpK36 | 2/2 | 1 | 2 | Quantification purpose | (Landman, et al., 2009) | |
| Multiplex real-time PCR | TEM and SHV (ESBL variants), CTX-M | NA | 1 | 3.5 | Commercial kit (CheckPoints) | (Nijhms, et al., 2012) |
| CIT, MOX, FOX, DHA, ACC, EBC | 6/SG | 1 | 3 | Performed with previous published primers | (Brolund, et al., 2010) | |
| CMY, ACT, DHA, MOX, ACC, FOX, 16S rRNA | 7/7 | 1 | 3 | No cross reaction with cAmpC of E. coli | (Geyer, et al., 2012) | |
| KPC, 16S rRNA | 2/2 | 1 | < 4 | From over-night cultures | (Singh, et al., 2012) | |
| IMP, VIM | 2/4 | 1 | < 1 | Specific detection | (Bisiklis, et al., 2007) | |
| KPC, RNaseP | 2/2 | 1 | 3 | Clinical implementation from blood cultures | (Hindiyeh, et al., 2011) | |
| KPC, TonB, GapA | 4/4 | 1 | 4 | Identifies peculiar K. pneumoniae sequencing types | (Chen, et al., 2012) | |
| GES, IMI/NMC, KPC, SME, OXA-48 | 5/5 | 1 | 3 | It does not discriminate the carbapenemase GES variants | (Swayne, et al., 2011) | |
| KPC, NDM, GES, OXA-48, IMP, VIM | 6/EG | 1 | 3 | Specific identification by Tm analysis | (Monteiro, et al., 2012) | |
| KPC, NDM, VIM, IMP, OXA-48 | NA | 1 | 3.5 | Commercial kit (CheckPoints). Not yet evaluated | NA | |
| QnrA/B/S/C/D, QepA | 6 | 2 | < 2 | Specific identification | (Guillard, et al., 2011) | |
| QnrA/B/ S | 3 | 1 | < 2 | Coupled with High resolution melting curve analysis | (Guillard, et al., 2012) | |
| Aac(6)-Ib-cr | 1/1 | 1 | < 1 | Coupled with high resolution melting curve analysis, specific detection | (Bell, et al., 2010) |
Note. NA, not available; SB, SYBR Green; EG, EvaGreen dye