TABLE 3.
Results of discordant PCR and culture specimens
| Discrepancy type and lab no. | Broad-range 16S rDNA method
|
Conventional method
|
Comment(s)g | |||
|---|---|---|---|---|---|---|
| PCR resulta | BLAST (% identity) | RDP-II (% similarity) | Microscopy resultb | Culture resultc | ||
| PCR-negative and culture- positive discrepancies | ||||||
| 1572 | − | NDf | ND | (−) | CNS (+) | Contamination* |
| 1705 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 1751 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 1818 | − | ND | ND | (−) | N. meningitidis (+) | Bacterial meningitis* |
| 1824 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 1961 | − | ND | ND | (−) | N. meningitidis (+) | Bacterial meningitis* |
| 2061 | − | ND | ND | (−) | L. monocytogenes (+) | Bacterial meningitis* |
| 2106 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 2225 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 2228 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 2251 | − | ND | ND | (−) | Pantoea species (+) | Contamination* |
| 2263 | − | ND | ND | (−) | CNS (+) | Contamination* |
| 2266 | − | ND | ND | GNC (+) | N. meningitidis (+) | Bacterial meningitis* |
| PCR-positive and culture- negative discrepancies | ||||||
| 1750 | + | S. pneumoniae (99.9) | S. pneumoniae (0.999) | (−) | (−) | Antibiotic treatment† |
| 2125 | +++ | S. agalactiae (99.7) | S. agalactiae (0.997) | (−) | (−) | Antibiotic treatment† |
| 2145 | +++ | P. bivia (98.5) | P. bivia (0.998) | (−) | (−) | Anaerobic culture not performed† |
| 2264 | ++ | N. meningitidis (99.8) | N. meningitidis (1.000) | (−) | (−) | Antibiotic treatment† |
| 2304 | +++ | S. pneumoniae (100) | S. pneumoniae (0.999) | (−) | (−) | Antibiotic treatment† |
| 2403 | +++ | S. pneumoniae (100) | S. pneumoniae (0.999) | (−) | (−) | Antibiotic treatment† |
| PCR and culture identifi- cation discrepancies | ||||||
| 1936d | + | Lactococcus sp. (87.8) | Neisseria sp. (0.925) | (−) | N. meningitidis (+) | SSEARCH result N. meningitidis |
| 2253e | +++ | F. nucleatum (99) | F. nucleatum (0.998) | GNC (+) | N. meningitidis (+) | PCR contamination |
The PCR result is reported as follows: +, weakly positive; ++, moderately positive; and +++, strongly positive. Numbers in parentheses are identity percentages.
GNC, gram-negative cocci. Symbols in parentheses reflect relative numbers of bacterial cells seen in direct microscopy: −, none; and +, sporadic.
Symbols in parentheses reflect relative numbers of colonies on the primary plate: +, few or enrichment broth positive; −, none.
An electropherogram showed clear signs of a mixed sequence and resulted in discrepant sequence results between BLAST and RDP-II. A third analysis with the SSEARCH algorithm identified N. meningitidis.
The sequencing result of F. nucleatum did not match the clinical presentation of the patient, although all controls were valid. Reanalysis of the original CSF and the original DNA isolate identified both N. meningitidis. The first result was therefore reported as contamination of the PCR reaction.
ND, not done.
*, Clinical interpretation; †, possible reason for negative culture.