Evaluation of the SpeeDx Carba (beta) multiplex real-time PCR assay for detection of NDM, KPC, OXA-48-like, IMP-4-like and VIM carbapenemase genes

Table 1 Oligonucleotides for in-house assays in this study

Set	Forward primer (5′-3′)	Reverse primer (5′-3′)	Probe	Reference
KPC^a	GGCCGCCGTGCAATAC	GCCGCCCAACTCCTTCA	FAM-TGATAACGCCGCCGCCAATTTGT-BHQ1	[18]
NDM^a	GACCGCCCAGATCCTCAA	CGCGACCGGCAGGTT	VIC-TGGATCAAGCAGGAGAT-MGB-NFQ	[18]
OXA-48-like	GTAGCAAAGGAATGGCAA	CCTTGCTGCTTATTcTCA^c	FAM-TCC(+A)GA(+G)CA(+C)AA(+C)TACG-Dabcyl	[19]
IMP-4-like^b	GGCAGTATTTCCTCTCATTT	GCAGCTCATTAGTTAATTCAG	FAM-CATAGTGACAGCACGGGCGGAAT-BHQ1	[20]
VIM^b	CGCGGAGATTGAGAAGCAAA	AGCCGCCCGAAGGACATC	HEX-TTGGACTTCCTGTAACGCGTGCA-BHQ1	[20]
16S rRNA^a	TGGAGCATGTGGTTTAATTCGA	TGCGGGACTTAACCCAACA	Quasar670-CACGAGCTGACGACARCCATGCA-BHQ2	[18]

^aKPC, NDM and 16S rRNA oligonucleotides were tested together in a multiplex PCR as previously described [18]
^bIMP-4-like and VIM oligonucleotides were tested together in a multiplex PCR as previously described [20]
^cThe lower case base differed to that of the original primer (C instead of G) and was substituted based on OXA-48-like sequence data on the Genbank database
‘+’ indicates locked nucleic acid (LNA) bases; MGB minor groove binder, BHQ black hole quencher, NFQ non-fluorescent quencher

ISSN: 1471-2334