Table 2.
Number and percent of results in agreement, disagreement, or undetected using the molecular method compared to the corresponding physician-ordered automated blood culture resulta
| Primer grouping | Total nb | Agreement |
Disagreement |
Not detected |
|||
|---|---|---|---|---|---|---|---|
| n | % | n | % | n | % | ||
| Staphylococcus spp.c | 51 | 50 | 98.0 | 1d | 0.0 | 0 | 2.0 |
| Streptococcus spp.e | 28 | 27 | 96.4 | 1f | 3.6 | 0 | 0.0 |
| Enteric GNRsg,h | 15 | 11 | 73.3 | 0 | 0.0 | 4i | 26.7 |
| Universal onlyj | 6 | 4 | 66.7 | 0 | 0.0 | 2 | 33.3 |
| All | 100 | 92 | 92 | 2 | 2.0 | 6 | 6.0 |
Numbers and percentages of the 100 isolates detected by PCR/pyrosequencing using a target-specific and/or universal primer set(s). Purified isolates were available for all 8 discordant samples; DNA extracts were analyzed using PCR/pyrosequencing, and all isolates were correctly identified using both the universal and target-specific primer sets (data not shown).
n, number of isolates.
Results for correct identification of Staphylococcus spp. are as follows: S. aureus (including both methicillin-sensitive S. aureus [MSSA] and methicillin-resistant S. aureus [MRSA]), 18/19 isolates (94.7%); CoNS, 32/32 isolates (100%).
While the universal primer set correctly classified the organism as a Staphylococcus sp., the DNA sequences generated using the Staphylococcus-specific primers failed to match any known sequence in our library or the GenBank database.
Results for correct identification of Streptococcus and Enterococcus spp. (n = 28) are as follows: GAS, 2/2 isolates (100%); GBS, 2/2 isolates (100%); GCS, 2/2 isolates (100%); GGS, 3/4 isolates (75%); Enterococcus spp., 8/8 isolates (100%); S. pneumoniae, 5/5 isolates (100%); viridans group streptococci, 5/5 isolates (100%).
Culture-based identification was GGS. While the universal primer set correctly classified the organism as a Streptococcus sp., the Streptococcus-specific primer set identified the organism as GCS. The difference in classification between GGS and GCS was a single base in the 233-bp region of the Streptococcus-specific 23S rRNA gene target being amplified.
GNRs, Gram-negative rods.
Results for correct identification of enteric GNRs (n = 15) are as follows: E. coli, 6/8 isolates (75%); Enterobacter/Citrobacter spp., 2/2 isolates (100%); S. marcescens, 1/1 isolate (100%); Salmonella sp., 1/1 isolate (100%); P. rettgeri, 1/1 isolate (100%); P. mirabilis, 0/1 isolate (0%); K. pneumoniae, 0/1 isolate (0%).
PCR/pyrosequencing reactions from both the universal primers and the enteric GNR primers failed to detect 2 E. coli isolates and 1 isolate each of P. mirabilis and K. pneumoniae.
Results for correct identification using the universal target only (n = 6) are as follows: P. aeruginosa, 3/4 isolates (75%); Bacillus sp., 1/1 isolate (100%); S. maltophilia: 0/1 isolate (0%).