A multiplex pneumonia panel for diagnosis of hospital-acquired and ventilator-associated pneumonia in the era of emerging antimicrobial resistance

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.

Evaluation of the clinical relevance of the Biofire© FilmArray pneumonia panel among hospitalized patients

PURPOSE

Panel PCR tests provide rapid pathogen identification. However, their diagnostic performance is unclear. We assessed the performance of the Biofire© FilmArray pneumonia (PN)-panel against standard culture in broncho-alveolar lavage (BAL) samples.

METHODS

Setting: University Hospital Basel (February 2019 to July 2020), including hospitalized patients with a BAL (± pneumonia). We determined sensitivity and specificity of the PN-panel against standard culture. Using univariate logistic regression, we calculated odds ratios (OR) for pneumonia according to PN-panel and culture status, stratifying by chronic pulmonary disease. We calculated ORs for pneumonia for different pathogens to estimate the clinical relevance.

RESULTS

We included 840 adult patients, 60% were males, median age was 68 years, 35% had chronic pulmonary disease, 21% had pneumonia, and 36% had recent antibiotic use. In 1078 BAL samples, bacterial pathogens were detected in 36% and 16% with PN-panel and culture, respectively. The overall sensitivity and specificity of the PN-panel was high, whereas the positive predictive value was low. The OR of pneumonia was 1.1 (95% CI 0.7-1.6) for PN-panel-positive only; 2.6 (95% CI 1.3-5.3) for culture-positive only, and 1.6 (95% CI 1.0-2.4) for PN-panel and culture-positive. The detection rate of Haemophilus influenzae, Staphylococcus aureus, and Moraxella catarrhalis in the PN-panel was high but not associated with pneumonia.

CONCLUSION

While sensitivity and specificity of PN-panel are high compared to culture, pathogen detection did not correlate well with a pneumonia diagnosis. Patients with culture-positive BAL had the highest OR for pneumonia-thus the impact of the PN-panel on clinical management needs further evaluation in randomized controlled trials.

Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card

Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.

Performance evaluation of a PCR panel (FilmArray® Pneumonia Plus) for detection of respiratory bacterial pathogens in respiratory specimens: A systematic review and meta-analysis

BACKGROUND

Accuracy and timing of antibiotic therapy remain a challenge for lower respiratory tract infections. New molecular techniques using Multiplex Polymerase Chain Reaction, including the FilmArray® Pneumonia Plus Panel [FAPP], have been developed to address this. The aim of this study is to evaluate the FAPP diagnostic performance for the detection of the 15 typical bacteria of the panel from respiratory samples in a meta-analysis from a systematic review.

METHODS

We searched PubMed and EMBASE from January 1, 2010, to December 31, 2022, and selected any study on the FAPP diagnostic performance on respiratory samples compared to the reference standard, bacterial culture. The main outcome was the overall diagnostic accuracy with sensitivity and specificity. We calculated the log Diagnostic Odds Ratio and analyzed performance for separate bacteria, antimicrobial resistance genes, and according to the sample type. We also reported the FAPP turnaround time and the out-of-panel bacteria number and species. This study is registered with PROSPERO (CRD42021226280).

RESULTS

From 10 317 records, we identified 30 studies including 8 968 samples. Twenty-one were related to intensive care. The overall sensitivity and specificity were 94% [95% Confidence Interval (CI) 91-95] and 98% [95%CI 97-98], respectively. The log Diagnostic Odds Ratio was 6.35 [95%CI 6.05-6.65]. 9.3% [95%CI 9.2-9.5] of bacteria detected in culture were not included in the FAPP panel.

CONCLUSION

This systematic review reporting the FAPP evaluation revealed a high accuracy. This test may represent an adjunct tool for pulmonary bacterial infection diagnostic and antimicrobial stewardship. Further evidence is needed to assess the impact on clinical outcome.

Evaluation of the BioFire® FilmArray® Pneumonia plus Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Method

Conventional methods used to determine pneumonia pathogens are characterized by low sensitivity and long turnaround times. Introducing new tests with better parameters in patients at higher risk of infections is highly anticipated. The results of the conventional quantitative culture method (CM) in determining the bacterial etiology of pneumonia were compared with the results of the Pneumonia plus Panel test (PNP; BioFire® Diagnostics, USA) in 79 samples of bronchoalveolar lavage (BAL). Materials were collected from 79 patients with suspected pneumonia treated in an oncologic hospital due to solid tumors. Only 16/79 BAL samples (20.3%) were true positive (TP) for bacterial etiology in CM vs. 27/79 samples (34.2%) true positive in the PNP test. The total agreement between methods of interpreting the result (positive or negative) was 84.8%. The most prevalent pathogens in both methods were Staphylococcus aureus, followed by Escherichia coli, Pseudomonas aeruginosa, and Haemophilus influenzae. The PNP test identified several respiratory pathogens that were not grown in culture. The semiquantitative value reported by the PNP test was higher than that reported by culture. The PNP test vs. combined test (PNP test and CM methods) demonstrated positive predictive value (PPV) and negative predictive value (NPV) values of 100.0% and 98.1%, and the sensitivity and specificity were 96.4% and 100.0%. The PNP test is a good tool for determining the etiology of bacterial pneumonia and may support the care of an oncologic patient. However, further large-sample studies are needed to research in strictly defined groups of oncologic patients.

Ten Issues to Update in Nosocomial or Hospital-Acquired Pneumonia: An Expert Review

Nosocomial pneumonia, or hospital-acquired pneumonia (HAP), and ventilator-associated pneumonia (VAP) are important health problems worldwide, with both being associated with substantial morbidity and mortality. HAP is currently the main cause of death from nosocomial infection in critically ill patients. Although guidelines for the approach to this infection model are widely implemented in international health systems and clinical teams, information continually emerges that generates debate or requires updating in its management. This scientific manuscript, written by a multidisciplinary team of specialists, reviews the most important issues in the approach to this important infectious respiratory syndrome, and it updates various topics, such as a renewed etiological perspective for updating the use of new molecular platforms or imaging techniques, including the microbiological diagnostic stewardship in different clinical settings and using appropriate rapid techniques on invasive respiratory specimens. It also reviews both Intensive Care Unit admission criteria and those of clinical stability to discharge, as well as those of therapeutic failure and rescue treatment options. An update on antibiotic therapy in the context of bacterial multiresistance, in aerosol inhaled treatment options, oxygen therapy, or ventilatory support, is presented. It also analyzes the out-of-hospital management of nosocomial pneumonia requiring complete antibiotic therapy externally on an outpatient basis, as well as the main factors for readmission and an approach to management in the emergency department. Finally, the main strategies for prevention and prophylactic measures, many of them still controversial, on fragile and vulnerable hosts are reviewed.

Prevalence and Clinical Characteristics of Bacterial Pneumonia in Neurosurgical Emergency Center Patients: A Retrospective Study Spanning 13 Years at a Tertiary Center

Patients with brain injuries are at a heightened susceptibility to bacterial pneumonia, and the timely initiation of empiric antibiotic treatment has been shown to substantially reduce mortality rates. Nevertheless, there is a need for knowledge regarding the resistance and prevalence of pulmonary bacterial infections in this patient population. To address this gap, a retrospective study was conducted at a neurosurgical emergency center, focusing on patients with brain injuries. Among the entire patient population, a total of 739 individuals (18.23%) were identified as having bacterial pneumonia, consisting of 1489 strains of Gram-negative bacteria and 205 strains of Gram-positive bacteria. The resistance of Klebsiella pneumoniae to imipenem exhibited a significant increase, rising from 21.74% in 2009 to 96.67% in 2018, and subsequently reaching 48.47% in 2021. Acinetobacter baumannii displayed resistance rates exceeding 80.0% against multiple antibiotics. The resistance profile of Pseudomonas aeruginosa was relatively low. The proportion of Staphylococcus aureus reached its peak at 18.70% in 2016, but experienced a decline to 7.83% in 2021. The abundance of Gram-negative bacteria exceeded that of Gram-positive bacteria by a factor of 5.96. Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococcus aureus are prominent pathogens characterized by limited antibiotic choices and scarce treatment alternatives for the isolated strains.