TABLE 1.
Comparison between the FilmArray pneumonia plus panel and standard-of-care reference testing results for LRT samples from COVID-19 patients with bacterial pneumoniaa
| Microbial target | No. positive by FA-PP and SoC/no. positive by SoC | PPA (%) (95% CI) | No. negative by FA-PP and SoC/no. negative by SoC | NPA (%) (95% CI) | No. positive only by FA-PP for samples from patients who wereb: |
|
|---|---|---|---|---|---|---|
| Under antimicrobial therapy | Not under antimicrobial therapy | |||||
| Bacterial species | ||||||
| Acinetobacter calcoaceticus-baumannii complex | 53/53 | 100 (93.2–100) | 159/159 | 100 (97.7–100) | ||
| Enterobacter cloacae complex | 4/4 | 100 (39.8–100) | 206/207 | 99.5 (97.4–100) | 1 | |
| Escherichia coli | 15/15 | 100 (78.2–100) | 195/196 | 99.5 (97.2–100) | 1 | |
| Haemophilus influenzae | 2/2 | 100 (15.9–100) | 208/209 | 99.5 (97.4–100) | 1 | |
| Klebsiella aerogenes | 5/5 | 100 (47.8–100) | 207/207 | 100 (98.2–100) | ||
| Klebsiella oxytoca | 2/2 | 100 (15.8–100) | 204/207 | 98.6 (95.9–99.7) | 1 | 2 |
| Klebsiella pneumoniae group | 23/23 | 100 (85.2–100) | 189/189 | 100 (98.1–100) | ||
| Proteus spp. | 2/2 | 100 (15.9–100) | 210/210 | 100 (98.3–100) | ||
| Pseudomonas aeruginosa | 19/19 | 100 (82.4–100) | 185/189 | 97.9 (94.8–99.4) | 4 | |
| Serratia marcescens | 6/6 | 100 (54.1–100) | 200/203 | 98.5 (95.8–99.7) | 2 | 1 |
| Staphylococcus aureus | 45/45 | 100 (92.1–100) | 155/161 | 96.4 (92.3–98.7) | 5 | 1 |
| Streptococcus agalactiae | 0/0 | NC | 208/210 | 99.1 (96.6–99.9) | 2 | |
| Streptococcus pneumoniae | 4/4 | 100 (39.8–100) | 206/207 | 99.5 (97.4–100) | 1 | |
| Total species | 180/180 | 100 (98.0–100) | 2,532/2,554 | 99.2 (98.7–99.5) | 14 | 8 |
| Antimicrobial resistance genes | ||||||
| CTX-M | 12/12 | 100 (73.5–100) | 200/200 | 100 (98.2–100) | ||
| KPC | 10/10 | 100 (69.2–100) | 202/202 | 100 (98.2–100) | ||
| mecA/-C and MREJc | 23/23 | 100 (85.2–100) | 185/187 | 98.9 (96.2–99.9) | 2 | |
| Total genes | 45/45 | 100 (92.1–100) | 587/589 | 99.7 (98.8–100) | 2 | |
Excluding off-panel organisms, FA-PP panel testing results were compared with those obtained by the SoC testing method that was used as the reference method. This method included bacterial identification, antimicrobial susceptibility testing, and (only for antimicrobial resistance genes) PCR-sequencing analysis, which were performed on the microbial species isolated in culture. FA-PP, FilmArray pneumonia plus panel; SoC, standard of care; LRT, lower respiratory tract; COVID-19, coronavirus disease 2019; PPA, positive percent agreement; NPA, negative percent agreement; CI, confidence interval; NC, not calculated.
The 22 species only detected by the FA-PP panel were from 19 LRT samples, of which 18 samples (13 monomicrobial and 5 polymicrobial by culture) each had one additional organism and 1 sample (polymicrobial by culture) had four additional organisms.
The FA-PP panel identifies methicillin-resistant S. aureus (MRSA) based on the detection of mecA/-C and MREJ (mec right-extremity junction).