Table 5. Results of EQA for PCR.
| Swab samplesa | FNA samplesb | Punch biopsy samplesc | Totald | |||||||||||
| INHe | DITMf | INHe | DITMf | INHe | DITMf | INHe | DITMf | |||||||
| DRB-PCRe | Standard PCRf | qPCRf | DRB-PCRe | Standard PCRf | qPCRf | DRB-PCRe | Standard PCRf | qPCRf | DRB-PCRe | Standard PCRf | qPCRf | Final resultg | ||
| Phase I h | Positivity rate i | N/A | 50.0% (3/6) | 0% (0/3) | N/A | 62.5% (10/16) | 16.7% (1/6) | N/A | 76.9% (10/13) | 33.3% (1/3) | N/A | 65.7% (23/35) | 16.7% (2/12) | 71.4% (25/35) |
| Case confirmation rate j | N/A | 18.8% (3/16) | 0% (0/16) | N/A | 43.8% (7/16) | 0% (0/16) | N/A | 12.5% (2/16) | 0% (0/16) | N/A | 75.0% (12/16) | 0% (0/16) | 75.0% (12/16) | |
| Phase II m | Positivity rate i | 78.8% (26/33) | 81.8% (27/33) | 16.7% (1/6) | 59.1% (26/44) | 66.0% (29/44) | 33.3% (5/15) | 59.1% (13/22) | 59.1% (13/22) | 0.0% (0/9) | 65.7% (65/99) | 69.7% (69/99) | 20.0% (6/30) | 75.8% (75/99) |
| False negative k | 3.0% (1/33) | N/A | N/A | 6.8% (3/44) | N/A | N/A | 0.0% (0/22) | N/A | N/A | 4.0% (4/99) | N/A | N/A | N/A | |
| Concordance rate l | 97.0% (32/33) | N/A | 93.2% (41/44) | N/A | 100% (22/22) | N/A | 96.0% (95/99) | N/A | N/A | |||||
| Case confirmation rate j | 30.3% (20/66) | 30.3% (20/66) | 0.0% (0/66) | 34.8% (23/66) | 39.4% (26/66) | 3.0% (2/66) | 6.1% (4/66) | 6.1% (4/66) | 0.0% (0/66) | 71.2% (47/66) | 75.8% (50/66) | 3.0% (2/66) | 78.8% (52/66) | |
| Total – phase I and II n | Positivity rate i | N/A | 76.9% (30/39) | 11.1% (1/9) | N/A | 65.0% (39/60) | N/A | 65.7% (23/35) | 8.3% (1/12) | N/A | 68.7% (92/134) | 19.0% (8/42) | 74.6% (100/134) | |
| Case confirmation rate j | N/A | 28.1% (23/82) | 0% (0/82) | N/A | 40.2% (33/82) | 2.4% (2/82) | N/A | 7.3% (6/82) | 0% (0/82) | N/A | 75.6% (62/82) | 2.4% (2/82) | 78.1% (64/82) | |
Table 5 shows results of external quality assurance for PCR. During the initial phase (phase I) PCR samples were analyzed at DITM by IS2404 standard PCR and IS2404 quantitative real-time PCR (qPCR). During the transitional phase (phase II) diagnostic sample pairs where analyzed in parallel at INH (IS2404 dry-reagent-based [DRB] PCR) and DITM as described for phase I. Positivity rates and case confirmation rates are provided for IS2404 DRB- and standard PCR, and additional diagnostic yields were calculated for IS2404 qPCR. N/A, not applicable.
Swab samples, DNA extract were prepared from swab samples.
FNA samples, DNA extract were prepared from fine-needle aspirate samples.
Punch samples, DNA extract were prepared from 3-mm punch biopsy samples.
Total per phase and laboratory.
INH applied IS2404-DRB-PCR. [21]
DITM applied standard, gel-based, IS2404 PCR [17] and IS2404 qPCR [27], [42] on all DNA extracts tested negative with standard PCR. For qPCR the additional diagnostic yield (i.e. the deviation of total final result from total result of standard PCR) were 5.7% (phase I) and 6.1% (phase II).
Final result of standard PCR and qPCR.
Phase I, initial phase of implementation of the national reference laboratory at INH from September through December 2010.
Positivity rate, number of positive samples divided by the total number of samples tested.
Case confirmation rate, number of laboratory confirmed BUD patients divided by the total number of suspected BUD cases.
Rate of false negative results at INH as determined by re-testing of DNA extracts at DITM by standard PCR.
Rate of concordant results from sample pairs at INH and DITM.
Phase II, transitional phase of implementation of the national reference laboratory at INH from January 2011 through April 2012.
Total results of the initial and the transitional phase.