Comparison of Roche Cobas Amplicor Mycobacterium tuberculosis Assay with In-House PCR and Culture for Detection of M. tuberculosis

DOI: 10.1128/JCM.36.7.2023-2029.1998

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Fig. 1.
Results of conventional testing of noninhibitory specimens.

Table 1.

Comparison of CA and in-house PCR with culture

Specimens	Amplification system	No. of culture-positive specimens^a that were PCR:		No. of culture-negative specimens^b that were PCR:		Sensitivity (%)	Specificity (%)	NPV (%)	PPV (%)
Specimens	Amplification system	Positive	Negative	Positive	Negative	Sensitivity (%)	Specificity (%)	NPV (%)	PPV (%)
All (n= 1,527)	CA	50	15	21	1,441	76.92	98.56	98.97	70.42
	In house	59	6	35	1,427	90.76	97.60	99.58	62.72
Smear positive	CA	27	1	1	3	96.42	75.00	75.00	96.42
(n = 32)^c	In house	28	0	3	1	100.00	25.00	100.00	90.32
Smear negative^d	CA	23	14	20	1,438	62.16	98.56	99.03	53.48
(n = 1,495)	In house	31	6	32	1,426	83.78	97.60	99.58	46.20

↵a Includes only specimens growingM. tuberculosis.
↵b Includes 10 culture-positive specimens growing MOTT.
↵c Includes specimens from TB patients only.
↵d Includes six unspecific positive smears and 10 smear-positive specimens from patients infected with MOTT.

Table 2.

Adjustment of discrepant results to the adapted gold standard

Test	No. of true-positive specimens for which:			No. of specimens for which positive PCR was not confirmable^b
Test	Positive PCR was confirmed by other culture-positive samples from same patient	Positive PCR was confirmed by other PCR	Negative PCR was confirmed by both PCRs^a
CA	15	2		4
In-house PCR	31	2		2
Acid-fast staining			1

↵a Smear-negative, culture-negative specimen from a patient with culture-proven TB.
↵b False-positive PCR.

Table 3.

Comparison of CA and in-house PCR to the adapted gold standard

Specimens	Amplification system	No. of adapted gold standard-positive specimens^a that were PCR:		No. of adapted gold standard-negative specimens^b that were PCR:		Sensitivity (%)	Specificity (%)	NPV (%)	PPV (%)
Specimens	Amplification system	Positive	Negative	Positive	Negative	Sensitivity (%)	Specificity (%)	NPV (%)	PPV (%)
All (n= 1,527)	CA	67	34	4	1,422	66.33	99.71	97.66	94.36
	In house	92	9	2	1,424	91.08	99.85	99.37	97.87
Smear positive	CA	28	4	0	0	87.50		99.37
(n = 32)^c	In house	31	1	0	0	96.87		99.37
Smear negative	CA	39	30	4	1,422	56.52	99.71	97.93	90.69
(n = 1,495)^d	In house	61	8	2	1,424	88.40	99.85	99.44	96.82

↵a Specimens from patients with TB (for a definition, see Materials and Methods).
↵b Specimens from patients without any evidence of TB.
↵c Includes only specimens from TB patients.
↵d Includes six unspecific positive smears and 10 smear-positive specimens from patients infected with MOTT.

Table 4.

Sensitivity of CA and in-house PCR compared to culture with different types of specimens

Specimen type	No. of all samples (sensitivity [%]) that were:			No. of smear-negative samples (sensitivity [%]) that were:
Specimen type	Culture positive	CA positive	In-house PCR positive	Culture positive	CA positive	In-house PCR positive
Sputum or BAL^a	23	17 (73.91)	19 (82.60)	11	5 (45.45)	7 (63.63)
Gastric aspirate	34	27 (79.41)	32 (94.11)	20	14 (70.00)	18 (90.00)
Urine	4	4 (100.00)	4 (100.00)	4	4 (100.00)	4 (100.00)
Other	4	2 (50.00)	4 (100.00)	2	0 (0)	2 (100.00)

Table 5.

Inhibition rates of CA with different specimen types

Specimen type^a	Total no. of specimens	No. of noninhibitory specimens	No. of inhibitory specimens	Inhibition rate (%)
Pus	47	45	2	4.25
Swab	32	31	1	3.12
Sputum or BAL^a	821	733	88	10.71
Gastric aspirate	354	309	45	12.71
Urine	157	153	4	2.54
Biopsy	86	83	3	3.48
Pleural fluid	122	113	9	7.37
CSF^b	29	29	0	0.00
Other	33	31	2	6.06
Total	1,681	1,527	154	9.16

Table 6.

Role of PCR for the primary diagnosis of TB and specification of positive smear results

Test(s) performed for primary diagnosis	No. of specimens	Comment
Microscopy plus CA or in-house PCR	4	Smear-positive MOTT infections
	4	Unspecific smear results
	17	Smear-positive TB cases
CA or in-house PCR	7	Smear-negative TB cases (including 2 culture-negative cases)
In-house PCR only	4	Smear-negative TB cases (including 3 missed by CA)
In-house PCR	2	False-positive PCR results
CA	4	False-positive PCR results
Total	42	Cases with a positive result by any of the investigated methods

Table 7.

Assessment of the minimum number of specimens necessary for CA for smear-negative TB patients

Patient	No. of specimens^a	No. of true-positive specimens^b	Rate of true-positive specimens (%)	No. of CA-positive specimens	Sequential no. of first CA-positive specimen^c	Localization of infection
55	4	4	100	4	1	Urogenital organs
543	5	5	100	2	1	Lungs
266	5	5	100	2	1	Lungs
176	1	1	100	1	1	Lungs
222	1	1	100	1	1	Lymph node
505	3	3	100	2	2	Lungs
287	10	1	10	1	7	Lungs
356	9	5	55.6	1	8	Lungs
354	3	3	100	0		Lungs
536	6	1	16.7	0		Mediastinal lymph node
587	3	1	33.3	0		Pulmonary lymph node

↵a Includes only specimens drawn from the site of infection before initiation of therapy. For details, see Materials and Methods.
↵b See also the definition of the adapted gold standard in Materials and Methods.
↵c As determined after ordering the specimens of each patient by the time of receipt.