Table 1. Results of LiPA compared with culture in detecting MTBC in primary clinical specimens*.
| Sample and AFB smear result | No. positive/no. tested (%) |
|||||
|---|---|---|---|---|---|---|
| Concordance | Sensitivity | Specificity | PPV | NPV | Mean days saved | |
| All primary LiPA | 1,667/1,922 (86.7) | 782/918 (85.2) | 886/1,004 (88.2) | 782/900 (86.9) | 886/1,022 (86.7) | 15.2 |
| Positive | 960/1,099 (87.4) | 747/798 (93.6) | 213/301 (70.8) | 747/835 (89.5) | 213/264 (80.7) | 14.8 |
| Negative | 679/792 (85.7) | 35/119 (29.4) | 644/673 (95.7) | 35/64 (54.7) | 644/728 (88.5) | 22.1 |
| Not done | 28/31 (90.3) | 0/1 (0) | 29/30 (96.7) | 0/1 (0) | 29/30 (96.7) | – |
| All primary LiPA (adjusted values)† | 1,667/1,828 (91.2) | 782/918 (85.2) | 886/921 (96.2) | 782/817 (95.7) | 886/1,022 (86.7) | 15.2 |
| Positive | 960/1,028 (93.4) | 747/798 (93.6) | 213/232 (91.8) | 747/766 (97.5) | 213/264 (80.7) | 14.8 |
| Negative | 679/771 (88.1) | 35/119 (29.4) | 644/659 (97.7) | 35/50 (70.0) | 644/728 (88.5) | 22.1 |
| Not done | 28/29 (96.6) | 0/1 (0) | 29/30 (96.7) | 0/1 (0) | 29/30 (96.7) | – |
| Respiratory | 1,168/1,298 (90.0) | 672/738 (91.1) | 496/560 (88.6) | 672/736 (91.3) | 496/562 (88.3) | 14.7 |
| Positive | 827/915 (90.4) | 657/696 (94.4) | 170/219 (77.6) | 657/706 (93.1) | 170/209 (81.3) | 14.5 |
| Negative | 328/369 (88.9) | 15/42 (35.7) | 313/327 (95.7) | 15/29 (51.7) | 313/340 (92.1) | 20.5 |
| Not done | 13/14 (92.9) | – | 13/14 (92.9) | 0/1 (0.0) | 13/13 (100.0) | – |
| Nonrespiratory | 499/624 (80.0) | 110/180 (61.1) | 390/444 (87.8) | 110/164 (67.1) | 390/960 (84.8) | 18.3 |
| Positive | 133/184 (72.3) | 90/102 (88.2) | 43/82 (52.4) | 90/129 (69.8) | 43/55 (78.2) | 17.2 |
| Negative | 351/423 (83.0) | 20/77 (26.0) | 331/346 (95.7) | 20/35 (57.1) | 331/388 (85.3) | 23.4 |
| Not done | 15/17 (88.2) | 0/1 (0) | 16/16 (100.0) | – | 16/17 (94.1) | –- |
| Biopsy specimen‡ | 92/108 (85.2) | 13/26 (50.0) | 79/82 (96.3) | 13/16 (81.3) | 79/92 (85.9) | 22.4 |
| Positive | 19/21 (90.5) | 10/10 (100.0) | 9/11 (81.8) | 10/12 (83.3) | 9/9 (100.0) | 24.1 |
| Negative | 72/86 (83.7) | 3/16 (18.8) | 69/70 (98.6) | 3/4 (75.0) | 69/82 (84.1) | 16.7 |
| Not done | 1/1 (100.0) | – | 1/4 (25.0) | – | 1/1 (100.0) | – |
| Gastric aspirate | 17/18 (94.4) | 4/5 (80.0) | 13/13 (100.0) | 4/4 (100.0) | 13/14 (92.9) | 16.8 |
| Positive | 8/8 (100.0) | 4/4 (100.0) | 4/4 (100.0) | 4/4 (100.0) | 4/4 (100.0) | 16.8 |
| Negative | 9/10 (90.0) | 0/1 (0.0) | 9/9 (100.0) | – | 9/10 (90.0) | – |
| Not done | – | – | – | – | – | – |
| Lymph node | 103/142 (72.5) | 50/68 (73.5) | 53/74 (71.6) | 50/71 (70.4) | 53/71 (74.6) | 18.7 |
| Positive | 54/79 (68.4) | 42/48 (87.5) | 12/31 (38.7) | 42/61 (68.9) | 12/18 (66.7) | 16.6 |
| Negative | 48/62 (77.4) | 8/20 (40.0) | 40/42 (95.2) | 8/10 (80.0) | 40/52 (76.9) | 29.6 |
| Not done | 1/1 (100.0) | – | 1/1 (100.0) | – | 1/1 (100.0) | – |
| Pleural fluid | 84/107 (78.5) | 5/23 (21.7) | 79/84 (94.0) | 5/10 (50.0) | 79/97 (81.4) | 26.8 |
| Positive | 6/10 (60.0) | 4/5 (80.0) | 2/5 (40.0) | 4/7 (57.1) | 2/3 (66.7) | 23.5 |
| Negative | 77/97 (79.4) | 1/18 (5.6) | 76/78 (97.4) | 1/3 (33.3) | 76/93 (81.7) | 40.0 |
| Not done | 1/1 (100.0) | – | 1/1 (100.0) | – | 1/1 (100.0) | – |
| Psoas abscess | 8/15 (53.3) | 3/6 (50.0) | 5/9 (55.6) | 3/7 (42.9) | 5/8 (62.5) | 19.0 |
| Positive | 2/3 (66.7) | 2/2 (100.0) | 0/1 (0.0) | 2/3 (66.7) | – | 17.0 |
| Negative | 6/12 (50.0) | 1/4 (25.0) | 5/8 (62.5) | 1/4 (25.0) | 5/8 (62.5) | 23.0 |
| Not done | – | – | – | – | – | – |
| Vertebral aspirate | 26/30 (86.7) | 10/12 (83.3) | 16/18 (88.9) | 10/12 (83.3) | 16/18 (88.9) | 15.4 |
| Positive | 9/10 (90.0) | 8/8 (100.0) | 1/2 (50.0) | 8/9 (88.9) | 1/1 (100.0) | 14.5 |
| Negative | 17/19 (89.5) | 2/3 (66.7) | 15/16 (93.8) | 2/3 (66.7) | 15/16 (93.8) | 19.0 |
| Not done | 0/1 (0.0) | 0/1 (0.0) | – | – | 0/1 (0.0) | – |
| Other§ | 169/204 (82.8) | 25/40 (62.5) | 145/164 (88.4) | 25/44 (56.8) | 145/160 (90.6) | 15.2 |
| Positive | 35/53 (66.0) | 20/25 (80.0) | 15/28 (53.6) | 20/33 (60.6) | 15/20 (75.0) | 15.1 |
| Negative | 122/138 (88.4) | 5/15 (33.3) | 117/123 (95.1) | 5/11 (45.5) | 117/127 (92.1) | 15.8 |
| Not done | 12/13 (92.3) | – | 13/13 (100.0) | – | 13/13 (100.0) | – |
*MTBC excludes 75 specimens containing substances inhibitory to the polymerase chain reaction (PCR), PCR-equivocal results, and samples with no definitive culture results (i.e., contaminated or not done). LiPA, line probe assay; MTBC, Mycobacterium tuberculosis complex; AFB, acid-fast bacilli; PPV, positive predictive value; NPV, negative predictive value. †Excludes samples from patients with a microbiologic diagnosis of MTBC made at the Mycobacterium Reference Unit in the last 18 or subsequent 3 months, and patients receiving antituberculous treatment currently or within the last 3 months. ‡Includes biopsy specimens from liver (n = 13), kidney (n = 2), skin (n = 15), lung (n = 20), pleura (n = 13), and miscellaneous sites (n = 45). §Includes ascites (n = 56), pericardial aspirates (n = 29), aspirates from miscellaneous sites (n = 80), blood (n = 1), bone marrow (n = 22), feces (n = 1), and urine (n = 15).