LETTER
Multiplex PCR panels are powerful tools for rapid pathogen identification in patients with respiratory tract (RT) infections (1–6). In particular, analysis of upper respiratory tract (URT) specimens with the BioFire Respiratory Panel 2 (BRP2), which primarily targets viruses, decreases time to pathogen detection, duration of antibiotic use, and hospital length of stay (7, 8). In addition, many clinical laboratories have validated the BRP2 on lower respiratory tract (LRT) specimens (9, 10). Recently, the BioFire Pneumonia Panel (BPN) was shown to accurately identify viruses as well as a broader array of bacteria in LRT specimens (11, 12). Clinical laboratories must now determine if the BRP2 or the BPN or both should be included in the test menu for LRT specimens, but data comparing of these assays in this context are not available. Here, we evaluate the performance of the BRP2 and the BPN on LRT samples from adults at a tertiary care academic medical center.
To assess the performance of the BRP2 and the BPN, each assay was run on 200 consecutively available LRT specimens collected at a tertiary care academic medical center from July 2018 through November 2018 (Table 1). These samples were evaluated retrospectively, and results were not reported to clinicians. Positive percent agreement (PPA) and negative percent agreement (NPA) were calculated using the BRP2 as the predicate method. Confidence intervals were constructed using the modified Wilson method implemented in DescTools package v0. 99.30 in R v3.5.2 (13–16).
TABLE 1.
Patient demographics and specimen informationa
Parameter | Value(s)b |
---|---|
Patient demographics | |
Median age in yrs (IQR) | 60.0 (39.7–80.3) |
Male | 125 |
Female | 74 |
Clinical information | |
Immunocompetent | 160 |
Immunocompromised | 40 |
Spontaneous breathing | 129 |
Mechanical ventilation | 71 |
Intensive care unit | 180 |
Emergency department | 13 |
Other hospital floor | 7 |
Specimen type | |
Bronchoalveolar lavage | 59 |
Bronchial wash | 11 |
Sputum | 54 |
Tracheal aspirate | 76 |
Patient sex was not specified for one specimen. IQR, interquartile range.
Data represent numbers of patients except where otherwise specified.
Regarding pathogens included on both panels and aggregating results by class, the PPA was 87% for viral targets (95% confidence interval [CI], 71% to 95%) and 100% for atypical bacterial targets (95% CI, 5% to 100%) (Table 2). The NPA was 100% for both viral and atypical bacterial targets (95% CI, 99% to 100%). In addition, 151 typical bacterial species were identified by the BPN but not the BRP2 (of note, these targets are included only on the BPN).
TABLE 2.
BRP2 and BPN agreementa
Class | Target | No. of specimens |
PPA (95% CI) |
NPA (95% CI) |
|||
---|---|---|---|---|---|---|---|
BRP2 positive BPN positive |
BRP2 positive BPN negative |
BRP2 negative BPN positive |
BRP2 negative BPN negative |
||||
Viruses | Adenovirus | 0 | 0 | 0 | 200 | NA | 100 (98–100) |
Coronavirusb | 3 | 0 | 0 | 197 | 100 (44–100) | 100 (98–100) | |
Human metapneumovirus | 3 | 0 | 0 | 197 | 100 (44–100) | 100 (98–100) | |
Human rhinovirus/enterovirus | 6 | 1 | 3 | 190 | 86 (49–99) | 98 (96–100) | |
Influenza A virus | 5 | 2 | 1 | 192 | 71 (36–95) | 99 (97–100) | |
Influenza B virus | 4 | 0 | 0 | 196 | 100 (51–100) | 100 (98–100) | |
Parainfluenza virus | 2 | 0 | 0 | 198 | 100 (18–100) | 100 (98–100) | |
Respiratory syncytial virus | 4 | 1 | 0 | 195 | 80 (38–99) | 100 (98–100) | |
Atypical bacteria | Chlamydia pneumoniae | 0 | 0 | 0 | 200 | NA | 100 (98–100) |
Mycoplasma pneumoniae | 1 | 0 | 0 | 199 | 100 (5–100) | 100 (98–100) | |
Overall | Viruses | 27 | 4 | 4 | 1,565 | 87 (71–95) | 100 (99–100) |
Atypical bacteria | 1 | 0 | 1 | 598 | 100 (5–100) | 100 (99–100) |
BRP2, BioFire Respiratory Panel 2; BPN, BioFire Pneumonia Panel; PPA, positive percent agreement; NPA, negative percent agreement; NA, not applicable.
Includes coronavirus HKU1, NL63, 229E, and OC43.
With respect to discordant results, influenza A virus was solely detected by the BRP2 in two specimens and by the BPN in one. All three of these specimens were positive for influenza A virus by the Cepheid Xpert Xpress Flu/RSV PCR assay, although cycle threshold (CT) values were near the limit of detection, suggesting low viral loads (Table 3) (17). Respiratory syncytial virus (RSV) was detected solely by the BRP2 in one specimen, which could not be evaluated by Flu/RSV PCR due to multiple invalid assay results. Rhinovirus/enterovirus was detected solely by the BRP2 in one specimen and by the BPN in three.
TABLE 3.
Specimens with discordant resultsa
Subject ID |
Target | BRP2 result |
BPN result |
Specimen | Location | Cepheid Xpert Xpress FLU/RSV |
CT |
|
---|---|---|---|---|---|---|---|---|
Flu A1 | Flu A2 | |||||||
WU006 | Influenza A virus | Negative | Positive | Bronchoalveolar lavage fluid | Non-ICU | Positive | 37.8 | 39.8 |
WU109 | Influenza A virus | Positive | Negative | Tracheal aspirate | ICU | Positive | 38.7 | 0 |
WU136 | Influenza A virus | Positive | Negative | Tracheal aspirate | ICU | Positive | 34.8 | 0 |
WU038 | Rhinovirus/enterovirus | Negative | Positive | Bronchoalveolar lavage fluid | ICU | Not tested | NA | NA |
WU052 | Rhinovirus/enterovirus | Negative | Positive | Sputum | ICU | Not tested | NA | NA |
WU154 | Rhinovirus/enterovirus | Negative | Positive | Sputum | ICU | Not tested | NA | NA |
WU054 | Rhinovirus/enterovirus | Positive | Negative | Sputum | ICU | Not tested | NA | NA |
WU014 | RSV | Positive | Negative | Tracheal aspirate | ICU | Invalid | NA | NA |
ID, identifier; BRP2, BioFire Respiratory Panel 2; BPN, BioFire Pneumonia Panel; CT, cycle threshold; Flu A1, influenza A virus target 1; Flu A2, influenza A virus target 2; ICU, intensive care unit; NA, not applicable; RSV, respiratory syncytial virus.
Here, we report that the BPN assay identified more typical bacterial pathogens in adult LRT specimens than the BRP2 while retaining comparable performance for viral targets. While agreement was also high among atypical bacterial targets, additional studies are needed given the small number of positive specimens. Overall, our results suggest that the BPN should be prioritized in the evaluation of LRT specimens and that simultaneous testing using both the BPN and the BRP2 is unlikely to result in clinically significant diagnostic gains.
ACKNOWLEDGMENT
This study was funded by BioFire Diagnostics.
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