Abstract
Diagnosis and management of bacterial pneumonia still relies on bacterial culture and antimicrobial susceptibility testing. The Unyvero Lower Respiratory Tract panel (LRT) is a multiplex molecular assay that provides results within approximately 4.5 hours. This study evaluated the analytical performance of the LRT on bronchoalveolar lavage (BAL) fluids and bronchial washings (BW) in a cancer patient population and retrospectively determined clinical impact on therapy. Sensitivity and specificity of LRT on BAL and BW compared with bacterial culture and susceptibilities were calculated. Chart reviews were performed to determine whether antibiotic management would have changed based on the LRT results. A total of 113 BAL and 123 BW respiratory samples from 191 patients were included. The overall sensitivity and specificity were 91.7% (95% CI, 77.5%-98.3%) and 92.0% (95% CI, 87.3%-95.4%), respectively. Staphylococcus aureus was the most common target detected (n = 21) with 89.5% (95% CI, 66.8%-98.7%) sensitivity and 98.2% (95% CI, 95.4%-99.5%) specificity. Based on availability of LRT results, 4.8% of patients could have been de-escalated faster. The LRT demonstrated an overall high accuracy for the detection of common bacteria associated with pneumonia. In this cancer inpatient cohort, treatment adjustment based on LRT results would have occurred in a small number of cases. Larger studies are necessary to understand the real-world impact within specific high-risk populations.
Lower respiratory tract infections (LRTI) are associated with significant morbidity and mortality in hospitalized patients.1 Factors that increase predisposition to LRTIs include comorbidities, length of hospitalization, and prolonged use of ventilators.1, 2, 3 In patients with hematopoietic stem cell transplant, liquid tumor patients, and neutropenic cancer patients, LRTI are the most common cause of death related to immunosuppressive therapy, conditioning regimens, graft-versus-host diseases, and treatment including immune response modulators.4
LRTIs are caused by a wide spectrum of microorganisms. Identification of the correct infectious etiology is necessary to ensure appropriate treatment. Culture remains the gold standard for diagnosis of LRTIs despite its relatively low sensitivity, particularly for fastidious organisms, and extended turn-around time to results (24 to 72 hours). Additionally, the yield of culture can be affected by pre-analytical variables that impacts organisms' viability including prior antibiotic exposure or specimen transport conditions.5, 6, 7 However, culture allows for the recovery of the organisms that are cultivable to perform antibiotic susceptibility testing (AST), thus allowing for targeted antibiotic management.
To circumvent some of the limitations of culture and improve the diagnosis of LRTIs, rapid multiplex assays that detect the most common organisms causing LRTIs were developed and recently received approval from the US Food and Drug Administration for use in clinical laboratories. These include the Curetis Unyvero Lower Respiratory Tract panel (LRT; Curetis, Holzgerlingen, Germany) and the BioFire FilmArray Pneumonia Panel (bioMérieux, Marcy-l'Etoile, France). Both multiplexed assays are moderately complex, sample-to-answer tests. The BioFire FilmArray Pneumonia Panel targets viral, bacterial, and antimicrobial resistance genes with a turn-around time to results of approximately 1 hour. The LRT detects 19 bacteria, 1 fungus, and 10 resistance markers with a turn-around time to results of 5 hours, significantly shorter than the typical 24 to 72 hours needed for culture and AST results.
The primary objective of this study was to evaluate the analytical performance of the LRT for BALs and BWs in a high-risk, cancer patient population. At the time of this study, the assay was Food and Drug Administration–approved only for tracheal aspirates and did not include Pneumocystis jirovecii (PJP), which has since been Food and Drug Administration–cleared for use with BAL and mini-BAL. Given the retrospective design of the study, a second objective was to evaluate the potential impact that rapid LRT results have on antibiotic management.
Materials and Methods
Patients and Specimens
Respiratory samples from patients receiving care at Memorial Sloan Kettering Cancer Center were enrolled for testing after completion of standard of care testing. Enrollment period was from February to August 2019. Inclusion criteria: i) specimens with sufficient volume for repeat testing if necessary, ii) collected within 24 hours prior to saving, iii) corresponding bacterial cultures ordered, and iv) unrestricted access to medical records available for review. Samples were stored at −20°C until testing on the Unyvero system. The study protocol was reviewed by the Memorial Sloan Kettering Cancer Center Institutional Review Board and granted a waiver of consent.
Unyvero Lower Respiratory Panel Testing
The following targets are included on the panel used for this study: Acinetobacter spp., Chlamydia pneumoniae, Citrobacter freundii, Enterobacter cloacae complex, Escherichia coli, Haemophilus influenzae, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella variicola, Legionella pneumoniae, Morganella morganii, Moraxella catarrhalis, Mycoplasma pneumoniae, Proteus spp., Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Stenotrophomonas maltophilia, and Streptococcus pneumoniae. The resistance genes included are: kpc, ndm, oxa-23, oxa-24, oxa-48, oxa-58, vim, ctx-M, mecA, and tem (Supplemental Table S1). The panel evaluated in this study did not include Pneumocystis jirovecii, which is currently included in the BAL LRT. All specimens were tested using the protocol provided by the manufacturer for endotracheal aspirates. In brief, 180 μL of respiratory sample was pipetted into a Unyvero sample tube containing the buffers needed for lysis in the Unyvero Lysator for 30 minutes, and then transferred to a Unyvero cartridge, which contains the reagents for extraction, amplification, and detection of DNA in the Unyvero Analyzer. If a panel resulted as invalid, the test was repeated once. Samples that tested invalid on repeat were excluded from the performance analysis of the assay.
Bacterial Culture
Lower respiratory samples were routinely cultured using blood agar, chocolate agar, MacConkey agar, colistin-nalidixic acid agar, and buffered charcoal yeast extract medium, and incubated under appropriate atmospheric conditions for up to 5 days in the WASPLab (Copan Diagnostics, Brescia, Italy). A 10-μL loop was used to inoculate culture plates using a 4-quadrant streaking pattern. Culture results were reported with quantitation as follows: 1+ (<10 colonies/plate), 2+ (10 to 50 colonies/plate), 3+ (50 to 299 colonies/plate), and 4+ (>300 colonies/plate). Sta. aureus was only reported if the quantity was above the pharyngeal flora background or if the penicillin-binding protein 2a (PBP2a) screen (Alere, Scarborough, ME) for methicillin-resistant Sta. aureus was positive. For the purpose of this study, the presence of a low quantity of Sta. aureus was recorded for comparison with the LRT results. Identification was performed by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry on the Vitek MS mass spectrometry system (bioMérieux).
AST
AST was performed using the MicroScan WalkAway system (Beckman Coulter, Brea, CA). For H. influenzae identified in respiratory specimens, only beta-lactamase testing was performed using the chromogenic cephalosporin Nitrocefin Cefinase test (Becton Dickinson, Franklin Lakes, NJ). Laboratory results were extracted from the laboratory information system.
BioFire FilmArray RP2 PCR Panel
Performance of the LRT for M. pneumoniae and Ch. pneumoniae was compared with the results obtained by the BioFire FilmArray Respiratory 2 Panel (RP2) (BioFire Diagnostics, Salt Lake City, UT) for which lower respiratory tract samples were validated off-label as previously described.8 Samples without a corresponding RP2 were excluded from the individual performance for these organisms.
Potential Impact on Antibiotic Management
To evaluate how the results of the LRT might have impacted antibiotic management in real time, an infectious disease expert (P.A.M.) retrospectively reviewed the electronic medical records for each patient. The following data were extracted: age, sex, location (outpatient versus inpatient) at time of sample collection, symptoms, underlying malignancy, the reason for the bronchoscopy (for infectious versus noninfectious workup), and antibiotic treatment. Criteria used to determine impact of LRT results on antibiotic management included: i) empiric antibiotic treatment, ii) relevance of organism identified (ie, H. influenzae possible pharyngeal flora contamination), and iii) the need for AST results to adjust antibiotic treatment.
Statistical Analysis
The sensitivity, the specificity, and overall agreement of the LRT and for each target in each samples type were calculated using culture and AST results as the gold standard (and the RP2 for M. pneumoniae and Ch. pneumoniae). Discordant results were resolved by performing a review of patient medical records for clinical or laboratory evidence of bacterial pneumonia. Analysis was performed with a Fisher's exact test. A P-value of <0.05 was considered significant. Data were analyzed in GraphPad Prism software version 8.4.2. (GraphPad Software, La Jolla, CA).
Results
Analytical Performance
A total of 242 respiratory samples were tested on the LRT. The performance characteristics of the LRT were calculated for a total of 236 samples (113 BALs and 123 BWs) after excluding 6 samples that included two invalids, one error, two patients with unavailable charts, and one without a corresponding bacterial culture. At least one target was detected in 49 of 236 samples (20.8%) by the LRT representing 12 BALs and 37 BWs compared with 33 of 236 samples (14.0%) positive by culture representing 7 BALS and 26 BWs. The overall percent agreement of the LRT with culture was 92.0% (95% CI, 87.7%-95.1%) and ranged from 90.2% (95% CI, 83.6%-94.9%) for BWs to 93.8% (95% CI, 87.7%-97.5%) for BALs. The sensitivity of the LRT on BALs was 77.8% (95% CI, 40.0%-97.2%) with a specificity of 95.2% (95% CI, 89.2%-98.4%). For BWs, the sensitivity was 96.3% (95% CI, 81.0%-99.9%) with a specificity of 88.5% (95% CI, 80.4%-94.1%) (Table 1).
Table 1.
Overall Performance Characteristics of the LRT on BAL and BW Samples in Comparison to Culture
| Specimen type | TP | FP | TN | FN | Total | Sensitivity (95% CI) | Specificity (95% CI) | OPA (95% CI) |
|---|---|---|---|---|---|---|---|---|
| BAL | 7 | 5 | 99 | 2 | 113 | 77.8% (40.0–97.2) | 95.2% (89.2–98.4) | 93.8% (87.7–97.5) |
| BW | 26 | 11 | 85 | 1 | 123 | 96.3% (81.0–99.9) | 88.5% (80.4–94.1) | 90.2% (83.6–94.9) |
| Total | 33 | 16 | 184 | 3 | 236 | 91.7% (77.5–98.3) | 92.0% (87.3–95.4) | 92.0% (87.7–95.1) |
BAL, bronchoalveolar lavage; BW, bronchial wash; FN, false negatives; FP, false positives; LRT, Lower Respiratory Tract panel; OPA, overall percent agreement; TN, true negatives; TP, true positives.
The most common target detected was Sta. aureus (n = 21/49; 42.9%) followed by P. aeruginosa (n = 9/49; 18.4%) and H. influenzae 7 (n = 7/49; 14.2%) (Table 2). Two of the 10 resistance genes were detected in tested specimens: mecA and tem. All three mecA results agreed with the reported Sta. aureus susceptibilities, whereas for all three tem detected along with H. influenzae, neither the organism nor beta-lactamase production was reported in culture. Positive percent agreement (PPA) and negative percent agreement for individual targets ranged from 89.5% (95% CI, 66.8%-98.7%) and 98.2% (95% CI, 95.4%-99.5%), respectively, for Sta. aureus to 100.0% and 97.9% to 100.0%, respectively, for all other targets detected (Table 2).
Table 2.
Cumulative Bacterial Target-Specific Performance of the LRT
| Organism | TP | FN | FP | TN | Positive percent agreement (95% CI) | Negative percent agreement (95% CI) |
|---|---|---|---|---|---|---|
| Acinetobacter species | 0 | 0 | 2 | 234 | N/A | 99.2 (97.0–99.9) |
| Citrobacter freundii | 1 | 0 | 0 | 235 | 100.0% (2.5–100.0) | 100.0% (98.4–100.0) |
| Chlamydia pneumoniae | 0 | 0 | 0 | 166∗ | N/A | 100.0% (97.8–100.0) |
| Escherichia coli | 1 | 0 | 2 | 233 | 100.0% (2.5–100.0) | 99.2% (97.0–99.9) |
| Haemophilus influenzae | 2 | 0 | 5 | 229 | 100.0% (15.8–100.0) | 97.9% (95.1–99.3) |
| tem† | N/A | N/A | N/A | N/A | N/A | N/A |
| Klebsiella oxytoca | 0 | 0 | 1 | 235 | N/A | 99.6% (97.7–100.0) |
| Klebsiella pneumoniae | 0 | 0 | 1 | 235 | N/A | 99.6% (97.7–100.0) |
| Moraxella catarrhalis | 0 | 0 | 2 | 234 | N/A | 99.2% (97.0–99.9) |
| Mycoplasma pneumoniae | 3 | 0 | 0 | 163∗ | 100.0% (29.2–100.0) | 100.0% (97.7–100.0) |
| Pseudomonas aeruginosa | 6 | 0 | 3 | 227 | 100.0% (54.1–100.0) | 98.7% (96.2–99.7) |
| Serratia marcescens | 1 | 0 | 0 | 235 | 100.0% (2.5–100.0) | 100.0% (98.4–100.0) |
| Staphylococcus aureus | 17 | 2 | 4 | 213 | 89.5% (66.8–98.7) | 98.2% (95.4–99.5) |
| mecA | 3 | 0 | 0 | 233 | 100.0% (29.2–100.0) | 100.0% (98.4–100.0) |
| Stenotrophomonas maltophilia | 1 | 0 | 4 | 231 | 100.0% (2.5–100.0) | 98.3% (95.7–99.5) |
| Streptococcus pneumoniae | 2 | 0 | 1 | 233 | 100.0% (15.8–100.0) | 99.6% (97.6–100.0) |
FP, false positives; FN, false negatives; LRT, Lower Respiratory Tract panel; N/A, not analyzed; TN, true negatives; TP, true positives.
Compared with BioFire RP2.
3/5 FP H. influenzae were also positive for tem.
A single bacterial target was detected in all 12 positive BAL samples (n = 12/12; 100%), whereas multiple bacterial targets were detected in BWs (n = 9/37; 24.3%). A total of 27 samples had either partial (n = 6, all BWs) or completely discordant (n = 20, 8 BALs and 13 BWs) results compared with culture (Table 3). Partial discordance was defined as agreement for at least one but not all targets detected, whereas complete discordance was defined as negative or completely different results between the two methods. Complete discordance was observed in eight BALs, with five of eight samples positive by the LRT only and three of eight samples positive by culture only. For the five LRT positive BALs, samples 1 to 4 were positive for a Gram-negative rod by the LRT, but cultures had no growth suggestive of a Gram-negative rod; only BAL-4 had a Gram-negative rod observed on Gram stain. BAL-5 was positive for Sta. aureus with 1+ Sta. aureus–like colonies in culture that were not further worked up per laboratory protocol. BALs samples 6 to 8 were culture positive but LRT negative. For the 13 BWs with completely discordant results, review of the culture work-up notes suggested that samples 1 to 6 might have been positive for the organism detected by the LRT but under the quantitative threshold for routine reporting. For samples 7 to 12, there was no evidence of the organism detected by the LRT in the culture. BW samples 13 to 14 were culture positive and LRT negative. Partial discordance was observed for six BWs. Culture work-up notes suggested that for BW samples 15 to 16, the discordant organisms may have been present in culture (based on colony morphology) but below the reportable thresholds, whereas for samples 17 to 19, there was no indication for the organism being present in culture.
Table 3.
Discordant Samples Data
| Sample | Discordance | LRT | Gram stain | Microbiology culture result |
|---|---|---|---|---|
| BAL-1 | Complete | Escherichia coli | 2+ GPCC, 2+ GPCPC | PHFL (negative MAC) |
| BAL-2 | Complete | Stenotrophomonas maltophilia | 1+ GPC | PHFL (negative MAC) |
| BAL-3 | Complete | Haemophilus influenzae/tem | NOS | PHFL absent, 1+ yeast |
| BAL-4 | Complete | Pseudomonas aeruginosa | 2+ GPCP, 1+ GNR | PHFL (negative MAC) |
| BAL-5 | Complete | Staphylococcus aureus | 2+ GPCPCC | PHFL (BAP: 1+ Sta. aureus-like) |
| BAL-6 | Complete | Negative | NOS | 1+ H. influenzae β-lactamase producer |
| BAL-7 | Complete | Negative | 1+ GPCPCC | 3+ Sta. aureus |
| BAL-8 | Complete | Negative | NOS | 1+ Sta. aureus |
| BW-1 | Complete | E. coli | 3+ GPCC | PHFL (MAC: 1+ LF) |
| BW-2 | Complete | H. influenzae | 2+ GPCPCC | PHFL (CHOC: 1+ grey colony) |
| BW-3 | Complete | P. aeruginosa | 3+ GPCC, 2+ GPR, 2+ GNR, 2+ GNDC | PHFL (MAC: 2+ NLF) |
| BW-4 | Complete | H. influenzae | NOS | PHFL (CHOC: 2+ yellow colonies) |
| BW-5 | Complete |
P. aeruginosa Sta. aureus Ste. maltophilia |
1+ GPCC | PHFL (BAP: 1+ Sta. aureus-like, MAC: 1+ NLF-2 morphologies) |
| BW-6 | Complete |
Sta. aureus Acinetobacter spp |
1+ GNDC, 1+ GPCPC | PHFL (Sta. aureus, MAC: 1+ NLF) |
| BW-7 | Complete | Sta. aureus | NOS | PHFL |
| BW-8 | Complete | Moraxella catarrhalis | NOS | PHFL |
| BW-9 | Complete | Klebsiella pneumoniae | NOS | PHFL (negative MAC) |
| BW-10 | Complete | H. influenzae | 1+ GPCPCC, 1+ GNR | Negative |
| BW-11 | Complete | Klebsiella oxytoca | 3+ GPCPC, 1+ GNR | PHFL (negative MAC) |
| BW-12 | Complete |
H. influenzae/tem Streptococcus pneumoniae |
3+ GPCPCC | PHFL |
| BW-13 | Complete | Negative | NOS | 4+ Sta. aureus |
| BW-14 | Complete | Negative | 2+ GPCPCC, 1+ GNR, 1+ GPR, 1+ GNDC | 1+ Methicillin-resistant Sta. aureus |
| BW-15 | Partial |
Ste. maltophilia Ci. freundii P. aeruginosa |
1+ GPCPCC, 1+ GPR | 3+ Ci. freundii complex, PHFL absent (MAC: 3 morphologies) |
| BW-16 | Partial |
P. aeruginosa Sta. aureus |
NOS | 1+ P. aeruginosa, PHFL (BAP: 1+ beta-hemolytic colonies) |
| BW-17 | Partial |
Sta. aureus/mecA Ste. maltophilia |
1+ GPC | 3+ Methicillin-resistant Sta. aureus (negative MAC) |
| BW-18 | Partial |
Acinetobacter spp E. coli |
1+ GPR, 1+ GNR | 3+ E. coli, PHFL |
| BW-19 | Partial |
Sta. aureus M. catarrhalis |
2+ GPCPCC, 1+ GPR | 1+ Sta. aureus, PHFL |
BAP, blood agar plate; CHOC, chocolate agar; GNDC, Gram-negative diplococci; GNR, Gram-negative rods; GPC, Gram-positive cocci; GPCC, Gram-positive cocci in clusters; GPCP, Gram-positive cocci in pairs; GPCPC, Gram-positive cocci in pairs and chains; GPCPCC, Gram-positive cocci in pairs, chains, and clusters; GPR, Gram-positive rods; LF, lactose-fermenter; LRT, Lower Respiratory Tract panel; MAC, MacConkey agar; NOS, no organisms seen; NLF, non-lactose fermenter; PHFL, pharyngeal flora.
Potential Clinical Impact of LRT
BALs, BWs, or both types of specimens were collected from 191 unique patients. Five patients (n = 5/191; 2.6%) had more than one specimen collected at different times during the study period. Thirty-six of 191 patients (18.8%) had both specimen types collected. A total of 75 of 191 patients (39.3%) had only BALs collected and 80 of 191 patients (41.9%) only had BWs collected. Median age of patients was 64 years (range, 19 to 89 years) with the majority (n = 133/191; 69.6%) diagnosed with solid tumor malignancies. Slightly more than half the patients (n = 106/191; 55.5%) were hospitalized at the time of sample collection with 34 of 106 (32.1%) in the intensive care unit (ICU). Medical records were reviewed to establish the potential of the LRT results to guide escalation or de-escalation of antibiotic treatment for these hospitalized patients only. Outpatients were excluded from this analysis because the turnaround time of the assay was not expected to provide a significant advantage over standard laboratory results to impact antibiotic management.
The LRT detected a bacterial target for 23 of 106 hospitalized patients including 10 of 23 in the ICU. Among the 23 patients with positive LRT results, empiric therapy was adequate for 52% (12/23), and results of the LRT would not have changed treatment (Table 4). For the other 11 patients, 5 of 11 patients were not on adequate empiric treatment with 3 of 5 patients requiring additional AST results to adjust antibiotic treatment correctly (eg, multidrug-resistant P. aeruginosa reported in culture), and 2 of 5 were not treated with no adverse health consequences. The remaining 6 patients were potentially on adequate empiric treatment, but AST results were required to optimize treatment.
Table 4.
Clinical Impact Assessment for Patients with Positive LRT
| Patient | ICU patient | LRT result | Adequate empiric coverage?∗ |
|---|---|---|---|
| 1 | Yes | Pseudomonas aeruginosa | Yes |
| 2 | Yes | Staphylococcus aureus | Yes |
| 3 | Yes | P. aeruginosa | No |
| 4 | Yes | Stenotrophomonas maltophilia | Yes |
| 5 | Yes |
Acinetobacter spp. Escherichia coli |
Maybe |
| 6 | Yes | Haemophilus influenzae | Yes |
| 7 | Yes | Sta. aureus | Yes |
| 8 | Yes | H. influenzae/tem | Yes |
| 9 | Yes | Klebsiella pneumoniae | Maybe |
| 10 | Yes | Klebsiella oxytoca | Yes |
| 11 | No | Sta. aureus | Yes |
| 12 | No | Sta. aureus | Yes |
| 13 | No | Sta. aureus | No |
| 14 | No | Mycoplasma pneumoniae | No |
| 15 | No | P. aeruginosa | No |
| 16 | No |
P. aeruginosa Sta. aureus Ste. maltophilia |
Maybe |
| 17 | No |
P. aeruginosa Sta. aureus |
Yes |
| 18 | No |
Sta. aureus/mecA Ste. maltophilia |
No |
| 19 | No |
M. pneumoniae Sta. aureus |
Yes |
| 20 | No |
H. influenzae/tem Streptococcus pneumoniae |
Yes |
| 21 | No | Sta. aureus | Maybe |
| 22 | No | P. aeruginosa | Maybe |
| 23 | No | Sta. aureus | Maybe |
ICU, intensive care unit; LRT, Lower Respiratory Tract panel.
Maybe, susceptibility testing results necessary to determine appropriateness of treatment; No, organism not being treated; Yes, organism detected covered by current treatment.
A total of 83 of 106 patients had negative LRT results with a respective negative bacterial culture; 24 of 83 were in the ICU. Among these 24 ICU patients, 21 of 24 patients had symptoms consistent with lower respiratory disease (ie, hypoxia, dyspnea, fever, cough) with 20 of 21 of these patients being on empiric treatment. In patients with high suspicion of infection, empiric treatment would have unlikely been discontinued based on negative culture and LRT results. A total of 6 of 24 ICU patients had other infectious etiologies reported not included in the LRT (2 PJP, 1 rhinovirus/enterovirus, 1 herpes simplex virus, 1 Pseudomonas putida, and 1 Corynebacterium striatum). In this group of ICU patients, only 1 patient was de-escalated based on negative laboratory results 3 days after broad-spectrum antibiotics had been initiated and may have been de-escalated sooner with the LRT.
For the 59 non-ICU patients with negative LRT results, a pulmonary infection was suspected in 43 of 59 patients with 31 receiving empiric treatment. A pathogen not included in the panel was found in 9 of 43 patients (2 PJP, 2 coinfected with PJP and rhinovirus/enterovirus, 2 Mycobacterium avium complex, 2 human metapneumovirus, 1 rhinovirus/enterovirus, and 1 coinfected with rhinovirus/enterovirus and cytomegalovirus). Antibacterial therapy was discontinued based on identification of PJP in 2 of 59 patients, and 1 patient of 59 was discontinued based on negative culture results. Overall, 4 of 83 patients with negative results (4.8%) were de-escalated.
Discussion
This study evaluates the analytical performance and potential utility of the LRT in a cancer patient population. The LRT had an overall sensitivity and specificity of 91.7% and 92.0%, respectively, with agreement for individual target ranging from 89.5% to 100.0%.
These results are in line with recent studies evaluating the performance of different versions of the LRT assay on BALs.7,9,10 Using the investigational use–only version of the Unyvero LRT, Collins et al9 reported a 96.5% PPA and 99.6% negative percent agreement for a total of 175 BAL samples tested. The positivity rate was higher with 74% (129/175) samples having at least one target detected compared with only 20.8% (49/236) in this current study. Of note, in this study, the sensitivity of the LRT in BAL fluid was lower than in BW specimens, but the overall number of positive BAL samples was small. Similarly, the most common bacterial target detected was Sta. aureus with a comparable PPA of 91.9%, followed by P. aeruginosa also with a 100% PPA.9 An evaluation of the LRT BAL application, which includes PJP, reported a sensitivity of 85.7% and a specificity of 98.4% for 620 respiratory specimens including BAL and endotracheal aspirates.7 Again, Sta. aureus was most commonly detected followed by P. aeruginosa; however, the sensitivity for these targets were at 86.5% and 88.9%, respectively.7 A multicenter study assessing the performance of the LRT BAL application panel reported an overall PPA and negative percent agreement of 93.4% and 98.3%, respectively, for a total of 1408 samples (1016 prospective and 392 archived samples).10 P. aeruginosa had the highest detection rate followed by Sta. aureus with PPA of 96.1% and 92.2%, respectively.10
Several studies have shown the utility of rapid multiplex molecular respiratory assays in improving appropriateness of treatment,11, 12, 13 although improvements in turn-around time do not always create a positive impact on the empirical treatment of patients.14 Because recovery in culture can be challenging, empiric treatment is often initiated, particularly when suspicion for infection is high. In this study, the potential for results of the LRT to guide clinical management was assessed and predicted to have limited impact. A total of 68% of inpatients were on empiric therapy. For patients with positive LRT results, empiric therapy either covered the organism identified or additional susceptibility would have been necessary for more targeted treatment, resulting in diminished impact for the LRT. Pulmonary infection was highly suspected in 77% of patients that were negative by LRT and culture. Among these, antibiotics were de-escalated in 4.8% of these patients based on a positive PJP PCR result or negative cultures. Of note, the current LRT BAL application includes PJP and may have a greater impact on patient management by providing rapid detection of PJP.
The clinical impact assessment findings in this study differed from other reports that have demonstrated de-escalation of broad-spectrum antibiotics in >50% of patients.7,15,16 A retrospective impact assessment of the Unyvero P55 panel (available in Europe) involving 28 ICU patients predicted that in 53.6% of patients who had antibiotic changes based on laboratory results, the panel would have prompted quicker adjustments.16 Jamal et al15 conducted a prospective study on the impact on antibiotic management for 49 patients (ICU and non-ICU included), and in 67.3% of cases, treatment was changed within 6 hours of specimen collection with 62.2% of patients showing improvement. Pickens et al7 predicted de-escalation based on results obtained from the Unyvero panel to be applicable in 66% of cases (405/615) evaluated. Similarly, the BioFire Pneumonia Panel has also shown potential to discontinue or de-escalate antibiotics with a study showing 48.2% patients could have had antibiotics discontinued or de-escalated, saving an average of 6 days of unnecessary administration of antibiotics.17
This study has some limitations. First, although samples were submitted for bacterial culture, infectious pneumonia might not have been high on the differential for several of these patients, explaining why all patients were on empiric therapy and thus no change in management was necessary despite rapid LRT results. This suggests that testing using the LRT should be restricted to specific high-risk populations to maximize the clinical utility of the assay. This approach would reduce misinterpretation of clinically irrelevant organisms that may prompt overuse of antibiotics. Second, discrepant results were not resolved by an alternative analytical method to confirm the presence or absence of organisms detected by the LRT. Of note, the biggest discrepancy occurred with H. influenzae and Sta. aureus, which depending on quantity may be considered part of the normal pharyngeal flora. The limit of detection of targets on the LRT ranged from 1.5 × 104 colony-forming units/mL (eg, Ch. pneumoniae) to 5 × 106 colony-forming units/mL (eg, Sta. aureus). Second, the current study was focused on an oncology adult patient population, which may in part contribute to the observed impact of the assay in patient management. Because many of the patients were receiving empiric treatment based on their predisposition to respiratory infections, the impact on their management can be hypothesized to be less influenced by this line of testing as it would be in a different patient population.
In conclusion, this study shows the high accuracy of the LRT on lower respiratory specimens (BALs and BW) for the rapid detection of common bacterial pneumonia etiologies. Although this line of testing may help tailor patient therapy to discontinue overuse of broad-range antibiotics, this may vary within specific patient populations. In oncology patients, especially immunocompromised and neutropenic patients, a more conservative approach in discontinuation or antibiotic adjustments may be applied due to the high predisposition to develop life-threatening infections. Thus, the authors predicted that only a small percentage of patients may benefit from the LRT assay. To clearly understand the impact of this assay, further studies, especially prospective studies, need to be conducted. Furthermore, implementation of this assay along with diagnostic and antimicrobial stewardship should be considered to support the interpretation of organisms that can be pathogenic or colonizers.
Acknowledgment
We thank Curetis for providing the instrumentation and reagents to conduct this study.
Footnotes
Supported in part by NIH/National Cancer Institute Cancer Center grant P30 CA008748 (M.C., P.A.M., N.E.B.). The manufacturer of the assay, Curetis, provided the instrumentation and reagents to conduct this study.
Disclosures: None declared.
Supplemental material for this article can be found at http://doi.org/10.1016/j.jmoldx.2021.08.002.
Author Contributions
All authors edited the manuscript and provided input on the data presented.
Supplemental Data
References
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