The Biofire® Filmarray® Pneumonia Plus panel for management of lower respiratory tract infection in mechanically-ventilated patients in the COVID-19 era: a diagnostic and cost-benefit evaluation

Potential Impact of Rapid Molecular Microbiologic Diagnosis for Mechanically Ventilated Children in Intensive Care With Suspected Pneumonia

BACKGROUND

Lower respiratory tract infections (LRTIs) remain a leading cause of community-acquired and nosocomial infection in children and a common indication for antimicrobial use and intensive care admission. Determining the causative pathogen for LRTIs is difficult and traditional culture-based methods are labor- and time-intensive. Emerging molecular diagnostic tools may identify pathogens and detect antimicrobial resistance more quickly, to enable earlier targeted antimicrobial therapy.

METHODS

This is a single-center, prospective observational laboratory study evaluating the use of the Biofire FilmArray pneumonia panel (FA-PP) (BioFire Diagnostics, Salt Lake City, UT) for bronchoalveolar lavage specimens from mechanically ventilated children admitted with suspected or presumed pneumonia. We aimed to determine its feasibility and utility for identifying pathogens, antimicrobial resistance and its potential influence on antibiotic prescribing.

RESULTS

We analyzed 50 samples taken from 41 children with a median age of 6 months. Positive agreement between culture and FA-PP was 83% and negative agreement was 76%. Agreement between FA-PP ( mecA/C or MREJ ) and culture was high for methicillin-resistant Staphylococcus aureus . In 3 cases, extended-spectrum beta-lactamase-producing Gram-negative organisms were detected by culture and not FA-PP. Hypothetically, FA-PP results would have affected antimicrobial prescribing in approximately half the cases (24, 48%).

CONCLUSIONS

FA-PP is a useful adjunct to traditional culture methods in mechanically ventilated children with LRTIs and may influence clinical decision-making regarding antibiotic escalation or stewardship.

Detection rate of herpes simplex virus DNA in the lower respiratory tract of critical care patients with or without coinfection determined by the Biofire® pneumonia plus panel

We investigated whether the results returned by the Biofire® Pneumonia Plus Panel (FA-PP) in lower respiratory tract specimens (LRT) specimens may identify patients who should be targeted for Herpes simplex virus (HSV) DNA testing. We included 35 adult ICU patients who underwent protocolized HSV DNA testing in LRT and/or plasma specimens by real-time PCR. Of these, one patient underwent allogeneic hematopoietic cell transplantation, one a kidney transplantation and one was under CAR-T cell therapy. Twenty-three of the 33 patients (69.6 %) had HSV-type 1 (HSV-1) DNA detected in LRT specimens (median viral load: 5.67 log10 copies/ml). Viral DNA was detected in 12/14 (85 %) plasma samples (median, 3.4 log10 copies/ml) from patients with HSV-1 DNA present in LRT specimens. Patients testing positive by the FA-PP had a non-significant (P = 0.28) higher rate of HSV-1 DNA detection (10/13; 77 %) compared with patients returning negative results (9/16; 56 %). In conclusion, requests for HSV DNA testing in ICU patients should not depend on the results of conventional culture methods nor those provided by the FA-PP.

Diagnostic Performance and Impact on Antimicrobial Treatment of a Multiplex Polymerase Chain Reaction in Critically Ill Patients With Pneumonia: A Multicenter Observational Study (The MORICUP-PCR Study: Morocco ICU Pneumonia-PCR study)

OBJECTIVES

Managing severe pneumonia remains a challenge. Rapid diagnostic tests, such as multiplex polymerase chain reaction (mPCR), facilitate quick microorganism identification and may enable timely and appropriate antimicrobial therapy. However, studies from low-income countries are scarce. This study aimed to evaluate the diagnostic characteristics of mPCR and its impact on antibiotic therapy and outcomes in critically ill patients with pneumonia.

DESIGN

Multicenter observational study.

SETTING

Twelve ICUs across Morocco.

PATIENTS

Adult patients with pneumonia requiring invasive mechanical ventilation, including community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-associated pneumonia (VAP).

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Respiratory samples were analyzed using both mPCR and conventional microbiological methods. The diagnostic performance of mPCR was evaluated, including its sensitivity and specificity. Additionally, the appropriateness of mPCR-induced modifications in empiric antibiotic therapy and their impact on patient outcomes were assessed. A total of 210 patients were included, with a median age of 50 years (range, 33-67 yr), of whom 66.2% were male. Pneumonia types were distributed as 30% CAP, 58% VAP, and 12% HAP. mPCR demonstrated a sensitivity of 96.9% (95% CI, 92.3-99.2%) and a specificity of 92% (95% CI, 91-93%). Following mPCR, antibiotic therapy modifications were observed in 58% of patients (n = 122), including de-escalation or cessation in 11% (n = 23), escalation in 26.5% (n = 56), adequacy adjustments in 7.5% (n = 16), and initiation of antibiotics in 13% (n = 27). The appropriateness of antibiotic therapy increased significantly from 38.7% (n = 83) to 67% (n = 141; difference, 27.5%; 95% CI, 18.3-36.7; p < 0.0001). Generalized mixed model analysis revealed that appropriate post-mPCR antibiotic therapy was associated with reduced mortality (adjusted odds ratio, 0.37; 95% CI, 0.15-0.93; p = 0.038).

CONCLUSIONS

Our findings suggest that the use of mPCR is associated with a significant improvement in the appropriateness of empiric antibiotic therapy and is also associated with a positive impact on the outcome of patients with pneumonia.

Impact of the microscopic quality of endotracheal aspirates on the performance of the Filmarray® pneumonia plus panel in intensive care unit patients with suspected lower respiratory tract infection

PURPOSE

We investigated how the microscopic quality of endotracheal aspirates (ETA) impacts the performance of the Filmarray® pneumonia plus panel (FA-PP) in patients undergoing mechanical ventilation (IMV) with suspicion of lower respiratory tract bacterial infection (LRTBI).

METHODS

The quality of ETA was categorized according to the number of leukocytes and buccal squamous epithelial (BSE)/field (100x magnification). G5 (< 10 BSE cells and > 25 leukocytes/field) and G4 (10-25 BSE cells and > 25 leukocytes/field) ETA were tested in parallel by the FA-PP and conventional semiquantitative culture.

RESULTS

In total, 153 ETA were graded as G5 (from 115 patients) and 56 as G4 (from 48 patients). Focusing on "conventional" bacterial species, a trend towards more positive results (P = 0.16), and co-detections (P = 0.18) was returned by G5 ETA. Although more targets were detected on G5 ETA (P = 0.005), the spectra of bacteria detected was comparable across G5 and G4 specimens. A trend towards higher bacterial burdens as quantitated by the FA-PP, and irrespective of the target, was observed in G5 (median, 106 genome copies/ml) vs. G4 ETA (median, 105 genome copies/ml). The degree of full agreement between FA-PP and culture was higher for G5 ETA (Kappa value, 0.54; 95% CI, 0.43-0.66) than for G4 ETA (Kappa value, 0.31; 95% CI, 0.11-0.49). For all bacterial targets detected, genome copy/ml numbers exceeded colony forming units (CFU)/ml counts in 1-2 log10, irrespective of ETA grading. The degree of correlation between genome copies/ml and CFU/ml was slightly better for G5 ETA (Rho = 0.65; P = 0.001) than for G4 ETA (Rho = 0.54; P = 0.11).

CONCLUSION

FA-PP testing of G5 ETA may provide more comprehensive and clinically useful information compared with G4 specimens in patients undergoing IMV with suspected LRTBI and receiving antimicrobial therapy. Yet G4 ETA may still provide useful microbiological information.

The role of rapid multiplex molecular syndromic panels in the clinical management of infections in critically ill patients: an experts-opinion document

Rapid multiplex molecular syndromic panels (RMMSP) (3 or more pathogens and time-to-results < 6 h) allow simultaneous detection of multiple pathogens and genotypic resistance markers. Their implementation has revolutionized the clinical landscape by significantly enhancing diagnostic accuracy and reducing time-to-results in different critical conditions. The current revision is a comprehensive but not systematic review of the literature. We conducted electronic searches of the PubMed, Medline, Embase, and Google Scholar databases to identify studies assessing the clinical performance of RMMSP in critically ill patients until July 30, 2024. A multidisciplinary group of 11 Spanish specialists developed clinical questions pertaining to the indications and limitations of these diagnostic tools in daily practice in different clinical scenarios. The topics covered included pneumonia, sepsis/septic shock, candidemia, meningitis/encephalitis, and off-label uses of these RMMSP. These tools reduced the time-to-diagnosis (and therefore the time-to-appropriate treatment), reduced inappropriate empiric treatment and the length of antibiotic therapy (which has a positive impact on antimicrobial stewardship and might be associated with lower in-hospital mortality), may reduce the length of hospital stay, which could potentially lead to cost savings. Despite their advantages, these RMMSP have limitations that should be known, including limited availability, missed diagnoses if the causative agent or resistance determinants are not included in the panel, false positives, and codetections. Overall, the implementation of RMMSP represents a significant advancement in infectious disease diagnostics, enabling more precise and timely interventions. This document addresses relevant issues related to the use of RMMSP on different critically ill patient profiles, to standardize procedures, assist in making management decisions and help specialists to obtain optimal outcomes.

Antibiotic stewardship with multiplex PCR for pneumonia in intensive care patients: A retrospective study

BACKGROUND

Early initiation of targeted antibiotic therapy is important to achieve the best patient outcomes in intubated patients with pneumonia in the intensive care unit (ICU). This study aimed to investigate the applicability of multiplex polymerase chain reaction (PCR) in an ICU by comparing the test results to the results of conventional microbiological methods to assess the possible impact on antibiotic therapy.

METHOD

This retrospective study investigated adult patients with pneumonia on mechanical ventilation in the ICU. Tracheal aspirates were collected within 24h after intubation and the initiation of mechanical ventilation. Samples were initially tested by conventional microbiological methods and subsequently re-evaluated with rapid multiplex PCR on stored samples. Concordance between the two methods was assessed. An intensivist and a microbiologist retrospectively reviewed the patients' electronic health records for relevant clinical details to evaluate the potential impact of multiplex PCR results on antibiotic therapy.

RESULTS

In this study, 76 patients were enrolled and 55 (72.4%) tested positive for 95 pathogens using multiplex PCR, while conventional microbiological methods identified 40 pathogens in 32 (42.2%) patients. Concordance between the two methods was observed in 42 (55.3%) patients. Multiplex PCR detected 39 additional pathogens in 31 (40.7%) patients. Retrospective analysis indicated potential antibiotic de-escalation in 35 (46.1%) patients and escalation in 4 (5.3%) patients. Multiplex PCR significantly reduced the turnaround time for test results.

CONCLUSION

In ICU patients with suspected pneumonia, multiplex PCR identified a higher number of pathogens compared to CMM. A retrospective assessment indicates that the use of multiplex PCR could potentially have prompted the de-escalation of antibiotic therapy in nearly half of the patients. Therefore, multiplex PCR may serve as a supplement to CMM in guiding antibiotic stewardship.

Rapid Molecular Diagnostics of Pneumonia Caused by Gram-Negative Bacteria: A Clinician's Review

With approximately half a billion events per year, lower respiratory tract infections (LRTIs) represent a major challenge for the global public health. Among LRTI cases, those caused by Gram-negative bacteria (GNB) are associated with a poorer prognostic. Standard-of-care etiologic diagnostics is lengthy and difficult to establish, with more than half of cases remaining microbiologically undocumented. Recently, syndromic molecular diagnostic panels became available, enabling simultaneous detection of tens of pathogen-related and antimicrobial-resistance genetic markers within a few hours. In this narrative review, we summarize the available data on the performance of molecular diagnostics in GNB pneumonia, highlighting the main strengths and limitations of these assays, as well as the main factors influencing their clinical utility. We searched MEDLINE and Web of Science databases for relevant English-language articles. Molecular assays have higher analytical sensitivity than cultural methods, and show good agreement with standard-of-care diagnostics regarding detection of respiratory pathogens, including GNB, and identification of frequent patterns of resistance to antibiotics. Clinical trials reported encouraging results on the usefulness of molecular assays in antibiotic stewardship. By providing early information on the presence of pathogens and their probable resistance phenotypes, these assays assist in the choice of targeted therapy, in shortening the time from sample collection to appropriate antimicrobial treatment, and in reducing unnecessary antibiotic use.

Optimizing patient outcomes in severe pneumonia: the role of multiplex PCR in the treatment of critically ill patients

Herein, we evaluated the optimal timing for implementing the BioFire® FilmArray® Pneumonia Panel (FA-PP) in the medical intensive care unit (MICU). Respiratory samples from 135 MICU-admitted patients with acute respiratory failure and severe pneumonia were examined using FA-PP. The cohort had an average age of 67.1 years, and 69.6% were male. Notably, 38.5% were smokers, and the mean acute physiology and chronic health evaluation-II (APACHE-II) score at initial MICU admission was 30.62, and the mean sequential organ failure assessment score (SOFA) was 11.23, indicating sever illness. Furthermore, 28.9, 52.6, and 43% of patients had a history of malignancy, hypertension, and diabetes mellitus, respectively. Community-acquired pneumonia accounted for 42.2% of cases, whereas hospital-acquired pneumonia accounted for 37%. The average time interval between pneumonia diagnosis and FA-PP implementation was 1.9 days, and the mean MICU length of stay was 19.42 days. The mortality rate was 50.4%. Multivariate logistic regression analysis identified two variables as significant independent predictors of mortality: APACHE-II score (p = 0.033, OR = 1.06, 95% CI 1.00-1.11), history of malignancy (OR = 3.89, 95% CI 1.64-9.26). The Kaplan-Meier survival analysis indicated that early FA-PP testing did not provide a survival benefit. The study suggested that the FA-PP test did not significantly impact the mortality rate of patients with severe pneumonia with acute respiratory failure. However, a history of cancer and a higher APACHE-II score remain important independent risk factors for mortality.

Advancing Pathogen Identification: The Role of Digital PCR in Enhancing Diagnostic Power in Different Settings

Digital polymerase chain reaction (dPCR) has emerged as a groundbreaking technology in molecular biology and diagnostics, offering exceptional precision and sensitivity in nucleic acid detection and quantification. This review highlights the core principles and transformative potential of dPCR, particularly in infectious disease diagnostics and environmental surveillance. Emphasizing its evolution from traditional PCR, dPCR provides accurate absolute quantification of target nucleic acids through advanced partitioning techniques. The review addresses the significant impact of dPCR in sepsis diagnosis and management, showcasing its superior sensitivity and specificity in early pathogen detection and identification of drug-resistant genes. Despite its advantages, challenges such as optimization of experimental conditions, standardization of data analysis workflows, and high costs are discussed. Furthermore, we compare various commercially available dPCR platforms, detailing their features and applications in clinical and research settings. Additionally, the review explores dPCR's role in water microbiology, particularly in wastewater surveillance and monitoring of waterborne pathogens, underscoring its importance in public health protection. In conclusion, future prospects of dPCR, including methodological optimization, integration with innovative technologies, and expansion into new sectors like metagenomics, are explored.

Breaking Boundaries in Pneumonia Diagnostics: Transitioning from Tradition to Molecular Frontiers with Multiplex PCR

The advent of rapid molecular microbiology testing has revolutionized infectious disease diagnostics and is now impacting pneumonia diagnosis and management. Molecular platforms offer highly multiplexed assays for diverse viral and bacterial detection, alongside antimicrobial resistance markers, providing the potential to significantly shape patient care. Despite the superiority in sensitivity and speed, debates continue regarding the clinical role of multiplex molecular testing, notably in comparison to standard methods and distinguishing colonization from infection. Recent guidelines endorse molecular pneumonia panels for enhanced sensitivity and rapidity, but implementation requires addressing methodological differences and ensuring clinical relevance. Diagnostic stewardship should be leveraged to optimize pneumonia testing, emphasizing pre- and post-analytical strategies. Collaboration between clinical microbiologists and bedside providers is essential in developing implementation strategies to maximize the clinical utility of multiplex molecular diagnostics in pneumonia. This narrative review explores these multifaceted issues, examining the current evidence on the clinical performance of multiplex molecular assays in pneumonia, and reflects on lessons learned from previous microbiological advances. Additionally, given the complexity of pneumonia and the sensitivity of molecular diagnostics, diagnostic stewardship is discussed within the context of current literature, including implementation strategies that consider pre-analytical and post-analytical modifications to optimize the clinical utility of advanced technologies like multiplex PCR.

Practice Versus Potential: The Impact of the BioFire FilmArray Pneumonia Panel on Antibiotic Use in Children

BACKGROUND

The BioFire FilmArray Pneumonia Panel (BFPP), a multiplex PCR panel for the diagnosis of lower respiratory tract infections, has been proposed as a tool for antimicrobial stewardship. Few studies evaluate real-world implementation of the BFPP and no studies focus exclusively on children. Our institution implemented BFPP testing without restrictions.

METHODS

We conducted a retrospective cohort study in children hospitalized at St. Louis Children's Hospital to (1) characterize the use of the BFPP in pediatric patients and (2) assess how results impacted antibiotic use. We included all BFPP tests obtained during the first year after the introduction of the test, September 2021 through August 2022. The primary outcome was change in antibiotic therapy within 24 hours of results, which was compared to the potential change in antibiotic therapy determined by two infectious diseases clinicians.

RESULTS

One hundred sixty-nine tests from 126 patients were included. Nine patients were immunocompromised and 19 had chronic tracheostomy. The majority of tests were sent from tracheal aspirate specimens (92%) and from patients in an intensive care unit (94%). Only 51% of tests were obtained due to respiratory failure or suspected pneumonia. For 80% of test results, there was potential to change antibiotics, but change occurred in only 46% of tests in practice. Antibiotic escalation was more common (26%) than de-escalation (15%) or discontinuation (4.1%).

CONCLUSIONS

In a cohort of pediatric patients tested with the BFPP, the majority of tests were sent from tracheal aspirates and less than half of tests were associated with a change in antibiotics.

Molecular point-of-care devices for the diagnosis of infectious diseases in resource-limited settings - A review of the current landscape, technical challenges, and clinical impact

Molecular point-of-care (POC) tests offer high sensitivity, rapid turnaround times, relative ease of use, and the convenience of laboratory-grade testing in the absence of formal laboratory spaces and equipment, making them appealing options for infectious disease diagnosis in resource-limited settings. In this review, we discuss the role and potential of molecular POC tests in resource-limited settings and their associated logistical challenges. We discuss U.S. Food and Drug Administration approval, Clinical Laboratory Improvement Amendments complexity levels, and the REASSURED criteria as a starting point for assessing options currently available inside and outside of the United States. We then present POC tests currently in research and development phases that have potential for commercialization and implementation in limited-resource settings. Finally, we review published studies that have assessed the clinical impact of molecular POC testing in limited- and moderate-resource settings.

Supporting Clinical Decisions with Rapid Molecular Diagnostic Pneumonia Panel in Pediatric Intensive Care Unit: Single Center Experience in Turkiye

INTRODUCTION

Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. It is crucial to promptly conduct diagnostic investigations in order to determine the microbiological cause of pneumonia, since this is necessary to ensure the appropriate delivery of antibiotic therapy to each individual patient. We evaluated the results of a rapid molecular diagnostic pneumonia panel in children with LRTI in a pediatric intensive care unit (PICU).

PATIENTS AND METHODS

Rapid molecular diagnostic pneumonia panel (BioFire®, FilmArray Pneumonia Panel plus; FA-PP) findings (71 results from 46 children) in a tertiary care PICU between 2019 and 2023 were retrospectively reviewed.

RESULTS

At least one bacterial pathogen was detected in 57 cases. A total of 77% of children had underlying conditions. A total of 70.4% of children needed invasive mechanical ventilation and 54.4% had ventilator-associated pneumonia. Pseudomonas aeruginosa (50.8%), Acinetobacter calcoaceticus baumannii complex (42%), and Klebsiella pneumoniae (38.6%) were the most common pathogens detected with the FA-PP. Of the 33 cases diagnosed with VAP, more than one pathogen was identified in 65.9% of cases, with the most commonly identified bacteria being K. pneumoniae (43.1%), P. aeruginosa (38.6%), and Acinetobacter calcoaceticus baumannii complex (31.8%). According to the FA-PP results, the same antibiotic therapy was continued in 39.4% of cases, escalated in 54.5%, and de-escalated in 6.1%.

CONCLUSIONS

The utilization of the FA-PP has some beneficial effects, including more prompt delivery of findings compared to conventional approaches. Additionally, this approach enables the identification of resistance profiles in children diagnosed with pneumonia in the PICU. Consequently, these test results facilitate the organization of antibiotic treatment strategies, including escalation and de-escalation approaches. The detection of resistance patterns was exclusively determined via the implementation of molecular testing, prompting a reevaluation of the isolation technique in accordance with the obtained data.

Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia

BACKGROUND

Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance.

METHODS

We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared.

RESULTS

We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%).

CONCLUSION

The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.