Comparison of a Point-of-Care FilmArray Test to Standard-of-Care Microbiology Test in Diagnosis of Healthcare Associated Infections in a Tertiary Care Pediatric Intensive Care Unit

Detecting Respiratory Pathogens for Diagnosing Lower Respiratory Tract Infections at the Point of Care: Challenges and Opportunities

Lower respiratory tract infections (LRTIs) are a leading cause of mortality worldwide, claiming millions of lives each year and imposing significant healthcare costs. Accurate detection of respiratory pathogens is essential for the effective management of LRTIs. However, this process often relies on sputum analysis, which requires extensive pretreatment steps. The viscous nature and complex composition of sputum present additional challenges, especially in settings where a rapid diagnosis at the point of care is essential. In this review, we describe the main types of LRTI, highlighting different patient care pathway and points of care. We review current methods for liquefying sputum samples and provide an overview of current commercially available diagnostic tools used in hospitals for LRTI detection. Furthermore, we critically review recent advancements in the literature focused on detecting respiratory pathogens and mechanisms of antimicrobial resistance in sputum, including nucleic acid amplification tests, immunoassays and other innovative approaches. Throughout the paper, we highlight challenges and opportunities associated with developing new biosensor technologies tailored for detecting respiratory pathogens in lower respiratory specimens. By shedding light on these pressing issues, we aim to inspire scientific community to create innovative diagnostic tools to address the urgent healthcare burden of lung diseases.

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.

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.

The Role and Value of Professional Rapid Testing of Acute Respiratory Infections (ARIs) in Europe: A Special Focus on the Czech Republic, Poland, and Romania

This review aims to explore the role of professional diagnostic rapid testing of acute respiratory infections (ARIs), especially COVID-19 and influenza, ensuring proper disease management and treatment in Europe, and particularly in Czech Republic, Poland, and Romania. The paper was constructed based on a review of scientific evidence and national and international policies and recommendations, as well as a process of validation by four experts. The development of new testing technologies, treatment options, and increased awareness of the negative multidimensional impact of ARI profiles transformed differential diagnosis into a tangible and desirable reality. This review covers the following topics: (1) the multidimensional impact of ARIs, (2) ARI rapid diagnostic testing platforms and their value, (3) the policy landscape, (4) challenges and barriers to implementation, and (5) a set of recommendations illustrating a path forward. The findings indicate that rapid diagnostic testing, including at the point of care (POC), can have a positive impact on case management, antimicrobial and antibiotic stewardship, epidemiological surveillance, and decision making. Integrating this strategy will require the commitment of governments and the international and academic communities, especially as we identified room for improvement in the access and expansion of POC rapid testing in the focus countries and the inclusion of rapid testing in relevant policies.

Impact of Multiplex Polymerase Chain Reaction Test in Patients With Meningitis or Encephalitis

Background

The objective of this study was to evaluate the impact of the FilmArray meningitis/encephalitis panel (FAME) on length of stay (LOS) and duration of antimicrobial treatment in children and adults in a Japanese community hospital.

Methods

This retrospective cohort study was conducted in Japan between January 2016 and December 2022. We included hospitalized patients with cerebrospinal fluid (CSF) samples and those aged <2 months or who had 5 or more white blood cells/μL in the CSF. To compare the days of therapy (DOT) and LOS between the pre-FAME and FAME periods, multivariate Poisson regression analyses were conducted without an offset term.

Results

The number of cases undergoing pathogen-specific polymerase chain reaction increased from 3.7% in the pre-FAME period to 57.5% in the FAME period (P < .001). The pathogen identification rate also increased during the FAME period, from 0.4% to 18.7% (P < .001). While the antibacterial DOT was not statistically different between the 2 periods (adjusted rate ratio [aRR], 1.06 [95% confidence interval {CI}, 1.00-1.13]; P = .063]), the antiviral DOT was significantly shorter in the FAME period (aRR, 0.80 [95% CI, .71-.89]; P < .001).

Conclusions

This study revealed a significant reduction in antiviral use during the FAME period, whereas LOS and antibacterial use did not decrease. Given the possibility of factors (eg, the COVID-19 pandemic) affecting the epidemiology of meningitis and encephalitis, the indications and impact of the FAME test should be evaluated with continuous monitoring of the epidemiology of meningitis and encephalitis and its clinical impact.

The diagnostic utility of microscopic quality assessment of sputum samples in the era of rapid syndromic PCR testing

This prospective study assessed the value of initial microscopy evaluation of sputum samples submitted for rapid syndromic PCR-based testing. Bacterial detections by the BioFire FilmArray Pneumonia Panel plus in 126 high- and 108 low-quality sputum samples, based on initial microscopy evaluation in samples from patients with lower respiratory tract infections were compared. We found that high-quality samples had a higher proportion of bacterial detections compared to low-quality samples (P = 0.013). This included a higher proportion of detections of bacteria deemed clinically relevant by predefined criteria (70% and 55%, P = 0.016), as well as a higher proportion of detections of Haemophilus influenzae (36% and 20%, P = 0.010). High-quality samples also had more detections of bacteria with high semi-quantitative values. The study found no significant difference between high- and low-quality samples in the proportions of samples with a single species of bacteria detected, samples with a bacteria treated by the clinician, samples with detection of a proven etiology of community-acquired pneumonia by predefined criteria, the number of bacterial species detected, or the detection of Streptococcus pneumoniae, Moraxella catarrhalis, or Staphylococcus aureus. The results showed that 40% (95% CI 35%-47%) of the bacterial detections would have been missed if only high-quality samples were analyzed. This included 41% (27%-56%) of detections of S. pneumoniae, 33% (23%-45%) of detections of H. influenzae, 42% (28%-58%) of detections of S. aureus, and 37% (23%-54%) of detections of M. catarrhalis. These findings suggest that all sputum samples submitted for rapid syndromic PCR testing should be analyzed, regardless of initial microscopy quality assessment. (This study has been registered at ClinicalTrials.gov under registration no. NCT04660084.) IMPORTANCE Microscopic quality assessment of sputum samples was originally designed for sputum culture, and its applicability in today's workflow, which includes syndromic PCR testing, may differ. Addressing this crucial gap, our study emphasizes the need to optimize the use and workflow of syndromic PCR panels, like the BioFire FilmArray Pneumonia plus (FAP plus), in microbiology laboratories. These advanced PCR-based tests offer rapid and comprehensive pathogen detection for respiratory infections, yet their full potential remains uncertain. By comparing bacterial detections in high- and low-quality sputum samples, we underscore the importance of including low-quality samples in testing. Our findings reveal a significant proportion of potentially clinically relevant bacterial detections that would have been missed if only high-quality samples were analyzed. These insights support the efficient implementation of syndromic PCR panels, ultimately enhancing patient care and outcomes.