. 2011 Nov;13(6):583–604. doi: 10.1016/j.jmoldx.2011.05.011

Table 4.

Other Organisms and Culture Confirmations

Organism	Specimen/sample type	Platform/assay (FDA no.)	Method	Target	Linear range (%)^⁎
Organism	Specimen/sample type	Platform/assay (FDA no.)	Method	Target	Sensitivity	Specificity
HCV quantitative	EDTA plasma or serum	COBAS AmpliPrep/COBAS TaqMan HCV Test (P060030)^†	Real-time RT-PCR	Transcript of a 244-base sequence in the highly conserved 5′ untranslated region of HCV; genotypes 1–6	43–69,000,000 IU/mL
HCV quantitative	Plasma or serum extracted from blood collected using EDTA or ACD	VERSANT HCV RNA 3.0 Assay (P020022)^‡	bDNA	5′UTR and core regions of the HCV genome	3200–40,000,000 IU/mL
HCV qualitative	Plasma or serum	APTIMA HCV RNA Qualitative Assay (P020011)^§	Transcription- mediated amplification	5′UTR of the HCV genome	91.8–100	97.8–98.5
	EDTA plasma or serum	AMPLICOR HCV test, version 2.0 (P000010)^†	RT-PCR	5′UTR of the HCV genome	92–94	96–97
	EDTA plasma or serum	COBAS AMPLICOR HCV test, version 2.0 (P000012)^†	RT-PCR	5′UTR of the HCV genome	92–94	96–97
HBV quantitative	EDTA plasma or serum	COBAS TaqMan HBV Test (P050028)^†	Real-time PCR	Core-precore region of the HBV genome; primer pairs to genotypes A–G of HBV and the precore mutation	20–170,000,000 IU/mL
HBV quantitative	EDTA plasma or serum	RealTime HBV Assay (P080026)^¶	Real-time PCR	Surface (S) gene of the HBV genome; primer pairs to genotypes A–G of HBV	10–1,000,000,000 IU/mL
GBS	Vaginal and rectal swabs incubated in Lim broth overnight	BD MAX GBS assay and BD MAX System (K090191)^∥	Real-time PCR	124-bp region of the cfb gene	95	96.7
	Vaginorectal swab	IDI-Strep B (K022504)^∥	Real-time PCR SmartCycler system^⁎⁎	GBS cfb gene	94	95.9
	Vaginorectal swab	Xpert GBS (K060540)^⁎⁎	GeneXpert System (real-time PCR)^⁎⁎	3′ region adjacent to the cfb gene	91.1	96.0
	Directly from vaginal and rectal swabs or from LIM broth culture	Smart GBS test (K062948)^⁎⁎	Real-time PCR SmartCycler system^⁎⁎	DNA 3′ region adjacent to the cfb gene	Direct from swabs, 81.6	Direct from swabs, 96.4
		Smart GBS test (K062948)^⁎⁎	Real-time PCR SmartCycler system^⁎⁎	DNA 3′ region adjacent to the cfb gene	From Lim broth, 98.7	From Lim broth, 90.4
	Vaginal and rectal swabs incubated in Lim broth overnight	GBS PNA FISH (K082612)^††	PNA-FISH	16S rRNA of Streptococcus agalactiae	89.2–100	86.8–100
	Vaginal and anorectal swabs in Lim broth culture	AccuProbe Group B Streptococcus Culture Identification Kit (K974572)^§	Culture confirmation; hybridization protection assay	DNA probe that detects rRNA sequences unique to S. agalactiae	97.5	99.8
CA, GV, and TV	Vaginal sample	BD Affirm VPIII Microbial Identification Tests (K931374, K923133, K931151)^∥	Single-stranded DNA probes, hybridize with complementary rRNA target sequences to form hybrids	rRNA	CA, 80.6	CA, 98.2
					GV, 83.8	GV, 99.1
					TV, 92.8	TV, 99.9
Group A Streptococcus	Throat swab	GASDirect Test (K924715)§	Hybridization protection assay	rRNA	91.7	99.3
Bacterial identification from culture	Cultures	AccuProbe Neisseria gonorrhoeae (K895583)^§	Hybridization protection assay	rRNA	100	100
Bacterial identification from culture	Cultures	AccuProbe Listeria monocytogenes (K901397)^§	Hybridization protection assay	rRNA	100	99.7
Organisms causing sepsis: GPCC	GPCC-positive cultures	BD GeneOhm StaphSR (K071026)^∥	Real-time PCR	SCCmec and mecA gene; nucA gene	MRSA % positive agreement, 100	MRSA % negative agreement, 98.2–100
	GPCC-positive cultures	BD GeneOhm StaphSR (K071026)^∥	Real-time PCR	SCCmec and mecA gene; nucA gene	SA % positive agreement, 98.8–100	SA % negative agreement, 96.5
	GPCC-positive cultures	Xpert MRSA/SA BC (K082140)^⁎⁎	GeneXpert System (real-time PCR)^⁎⁎	Spa and mecA genes and SCCmec inserted into S. aureus chromosomal attB insertion site	MRSA, 98.3	MRSA, 99.4
	GPCC-positive cultures	Xpert MRSA/SA BC (K082140)^⁎⁎	GeneXpert System (real-time PCR)^⁎⁎		SA, 100	SA, 98.6
	GPCC-positive cultures	S. aureus PNA FISH (K060099)^††	FISH assay	Species-specific 16S rRNA of S. aureus^‡‡	100	100^‡‡
	GPCC-positive cultures	S. aureus/CNS PNA FISH (K092166)^††	FISH assay	Species-specific 16S rRNA of S. aureus^‡‡	100	100^‡‡
	GPCC-positive cultures	AccuProbe S. aureus (K902213)^§	Hybridization protection assay	rRNA	100	100
Organisms causing sepsis: GPCPC	GPCPC-positive cultures	AccuProbe Streptococcus pneumoniae (K902908)^§	Hybridization protection assay	rRNA	100	100
Organisms causing sepsis: GPCPC	GPCPC-positive cultures	E. faecalis/OE PNA FISH (K083074)^††	PNA; FISH assay	Species-specific 16S rRNA in E. faecalis and other enterococci^§§	% positive agreement with culture, 100	% negative agreement with culture, 100
Organisms causing sepsis: smears from GNR	GNR-positive cultures	EC, PA	PNA; FISH assay	Species-specific rRNA of EC and PA	EC, 100	100^¶¶
	GNR-positive cultures	PNA FISH (K081309, K092236)^††	PNA; FISH assay	Species-specific rRNA of EC and PA	PA, 97.5	100
	GNR-positive cultures	EC, KP, PA PNA FISH (K101558)^††	PNA; FISH assay	Species-specific rRNA of EC, KP, and PA	EC, 100	EC, 97.5
					KP, 98.7	KP, 97.5
					PA, 96.9	PA, 97.5
Organisms causing sepsis: yeast	Smears made directly from yeast-positive blood cultures	Candida albicans PNA FISH (K062461)^††	PNA FISH species-specific probes	16S rRNA of C. albicans	100	100
		Yeast Traffic Light PNA FISH (K080719)^††
		C. albicans/C. glabrata PNA FISH (K092784)^††
	Yeast-positive blood cultures	AccuProbe Blastomyces dermatitidis (K903201)^§	Hybridization protection assay	rRNA	98.1	99.7
		AccuProbe Coccidiodes immitis (K904047)^§			98.8	100
		AccuProbe Histoplasma capsulatum (K896859)^§			100	100
Mycobacterial identification from cultures	Growth from appropriate solid media or broth	AccuProbe M. avium (K896494)^§	Hybridization protection assay	rRNA	99.3	100
		AccuProbe M. avium complex (K897078)§			99.9	100
		AccuProbe Mycobacterium gordonae (K896492)^§			98.8	99.7
		AccuProbe Mycobacterium intracellulare (K897077)^§			100	100
		AccuProbe Mycobacterium kansasii (K904463)^§			98.0	96.8
		AccuProbe MTB complex (K896493)^§			99.2	99.9
Mycoplasma species	Tissue culture	Mycoplasma Tissue Culture NI (MTC-NI)	DNA probe	rRNA of Mycoplasma and Acholeplasma species	Not applicable	Not applicable
Mycoplasma species	Tissue culture	Rapid Detection System (K860574)^§	DNA probe	rRNA of Mycoplasma and Acholeplasma species	Not applicable	Not applicable

ACD, anticoagulant citrate dextrose; bDNA, branched DNA; CA, Candida species; EC, Escherichia coli; GNR, Gram-negative rod; GPCC, Gram-positive cocci in clusters; GPCPC, Gram-positive cocci in pairs and chains; GV, Gardnerella vaginalis; KP, Klebsiella pneumonia; PA, Pseudomonas aeruginosa; TV, Trichomonas vaginalis.

^⁎

Sensitivity, specificity, linearity range, and percentage positive or negative agreement with culture data are sourced from FDA submission material or product inserts.

^†

Obtained from Roche Molecular Diagnostics, Pleasanton, CA.

^‡

Obtained from Siemens Healthcare Diagnostics, Deerfield, IL.

^§

Obtained from Gen-Probe, Inc., San Diego, CA.

^¶

Obtained from Abbott Molecular, Inc., Des Plaines, IL.

^∥

Obtained from BD Diagnostics, Sparks, MD.

^⁎⁎

Obtained from Cepheid, Sunnyvale, CA.

^††

Obtained from AdvanDx, Inc., Woburn, MA.

^‡‡

False-positive results with Staphylococcus schleiferi may occur because of a single-base mismatch.

^§§

Enterococcus moraviensis is identified as E. faecalis because of sequence identity.

^¶¶

False-positive results may occur with Shigella species (serogroups A, B, C, or D), Escherichia albertii, and Escherichia fergusonii because of sequence similarity.