Acute lower respiratory infection (ALRI) remains the most important global public health problem amongchildren.1–3 ALRI was estimated to cause14.9 million episodes that resulted in pediatric hospital admissions worldwide in 20104 and around 650,000 deaths of young children in 2016.5 The disease is caused by a large and heterogeneous group of infections including bacterial, viral, and other etiologies. Although incidence of viral ALRI is larger at early ages,6,7 pathogenic respiratory bacteria produce higher morbidity and mortality rates globally, especially among older children.5 Occurrence of mixed ALRI is also common during childhood.8–10

Distinguishing the etiology of ALRI becomes challenging, since derived signs and symptoms are often unspecific. A gold standard for etiological diagnosis of ALRI has not yet been developed.11 Conventional microbiological diagnostic methods such as bacterial culture, targeted polymerase-chain reaction (PCR) assays and rapid viral antigen tests have limitations in comprehensiveness, accuracy, and/or timeliness of results to guide clinical decisions, even expanding the arsenal of diagnostic tools with chest radiographies and acute-phase reactant measurements.12,13

Treatment of children with viral ALRI appears to be an area where extensive misuse of antibiotics could be reduced.14 In the last years, the introduction of fast molecular assays for multiple identification of respiratory viruses and bacteria has offered clinicians the potential to identify the viral origin of ALRI that might otherwise be considered to have a bacterial etiology and thus be treated with antibiotics. The FilmArray® Respiratory Panel (BioFire Diagnostics Inc., US), hereafter FA RP, is a qualitative reverse transcriptase PCR panel assay that targets adenovirus (AdV), coronavirus (CoV) types 229E/NL63/OC43/HKU1, influenza A virus (IFV-A) including differentiation of subtypes H1/H1N1-2009/H3, influenza B virus (IFV-B), human metapneumovirus (HMPV), parainfluenza virus (PIV) types 1/2/3/4, respiratory syncytial virus (RSV) types A/B, rhinovirus/enterovirus (RV/EV), Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae in a single respiratory sample. FA RP integrates sample preparation, DNA amplification and detection into an automated process with only 2min of hands-on time and 1 hour of instrumentation time.15

The main aim of our study was to evaluate to which extent the utilization of FA RP improved etiological diagnosis of ALRI and subsequent antimicrobial prescribing practices in critical care pediatric patients, compared to a bundle of routine microbiological diagnostic assays.

Our study showed an increase in diagnostic yield, timeliness of results and judicious use of antimicrobials as a consequence of the implementation of FA RP for diagnosing ALRI, in comparison with conventional microbiological tests. To the best of our knowledge, these findings had not been previously reported in cohorts of critical care pediatric patients, a specific study group characterized by a noticeable proportion of bacterial ALRI and mixed ALRI etiologies.

An increase in diagnostic yield attributable to FA was observed in precedent studies that compared accuracy of the panel test with that of other viral panel tests16 and batched PCR assays.17 Nonetheless, previous diagnostic accuracy studies were mostly focused on adult cohorts or groups. On the other hand, FA RP median time to results observed in our study (2.9h) was consistent with outcomes reported in previous studies reporting a mean time of 3.1h18 or median times of 1.4h16,19 and 2.3h20 for FA RP testing.

Previous literature on the potential linkage of rapid respiratory panel testing with optimized antibiotic use shows discordant results. A study in pediatric and adult patients with uncomplicated ARI admitted to an Emergency Department during the influenza epidemic season described a decrease in antibiotic use of half a day after shifting from a set of multiplex and singleplex commercial PCR assays to FA RP.17 In contrast, a randomized controlled trial of adults presenting with ARI to the Emergency Department or acute medical unit of a large hospital over two winter seasons and tested either by FA RP or laboratory PCR tests reported that mean duration of antibiotics was similar in both groups.20 Similarly, a quasi-randomized study in adults hospitalized with upper respiratory infection or influenza-like illness, with or without lower respiratory infection, found no evidence of reductions in antibiotic utilization as a consequence of FA RP testing, compared to equivalent outcomes when testing was performed by an array of laboratory-developed multiplex and singleplex PCR assays.21 Moreover, an observational study conducted in a hospital that switched from a respiratory viral panel to FA RP for diagnosing adult patients with respiratory viral illnesses did not observe statistically significant differences in antibiotic use after the change in the diagnostic strategy, yet time to results decreased markedly from 24 to 12h.22

We speculate that we found a minor decline in antibiotic use directly associated to FA RP implementation because the presence of a respiratory virus detected by a panel test that covers an extensive set of viral targets but only certain atypical bacterial targets does not rule out a potential bacterial coinfection, particularly in a PICU environment where patients are highly vulnerable. The marked difference between proportions of bacterial ALRI etiologies confirmed by FA RP and the composite reference standard (1.5 vs. 11.5%) supports our hypothesis. Withdrawing or postponing antibiotic administration in the PICU before availability of negative bacterial culture results in the absence of a comprehensive bacterial and viral respiratory panel test appears unlikely, given the high risk of concomitant or secondary bacterial ALRI in severely ill children. Results suggest the need of combining FA RP with bacterium-targeted microbiological assays on appropriate pediatric respiratory specimens (bronchoalveolar lavage or endotracheal aspirates) for comprehensive etiological diagnosis of pediatric severe ALRI. In this regard, a general recommendation has been made for rapid molecular diagnostic tests to incorporate testing for relevant bacterial pathogens in addition to viral targets in order to limit antibacterial therapy.23 It is also to be noted that the manufacturer of FA RP has recently launched a pneumonia panel test that includes 18 bacterial pathogens, some of which are highly prevalent in bacterial ALRI.24

Interestingly, we observed that detection or not detection of Mycoplasma pneumoniae by FA RP was a factor leading to a change to a more targeted antibiotic therapy, either for escalation or de-escalation, in line with recommendations of clinical practice guidelines for treatment of community-acquired pneumonia in children.25 In a similar way, detection or not detection of IFV by the panel test guided discontinuation or start of antiviral treatment, as recommended by guidelines. It is worthwhile to highlight that IFV-positive samples by FA RP were not bacterial-positive by other microbiological assays and patients sampled did not show radiological findings or acute-phase reactant measurements that could suggest bacterial co-infection and thus remained off antibiotics, also in accordance with guidelines.

This study presents some limitations. First, it was a single-center study with a relatively low sample size, although the cohort was adequately characterized and monitored to infer consistent conclusions. Second, requests for routine tests were made at the discretion of clinicians. This aspect might induce a certain bias depending on individual preferences to order certain microbiological assays and not others. However, in our view the study reflects the real situation in a hospital environment where some variability in the selection of the best diagnostic strategy may exist among clinicians. Third, outcomes were obtained using an observational cohort design. Further analysis adopting experimental randomized designs would increase external validity of results.

In conclusion, diagnostic performance of FA RP improved accuracy and timeliness of ALRI etiological diagnosis in critical care pediatric patients, in comparison to routine microbiological tests. Implementation of the panel test enhanced a more rational use of antiviral and antibiotic drugs in those patients. However, non negligible occurrence of bacterial ALRI in children suggests the need to combine the panel test with other bacterium-targeted microbiological assays for comprehensive etiological diagnosis of pediatric severe ALRI.

Conflict of interest statement: CMA reports research grants to her institution from Qiagen, Biofire Diagnostics, Pfizer, Roche Diagnostics, BioMérieux, Alere and Genomica SAU, and compensation fees from Qiagen, Roche Diagnostics and BioMérieux for scientific presentations in satellite symposiums; PB reports compensation fees from Roche Diagnostics for scientific presentations in satellite symposiums. The rest of authors report no conflict of interest.

Funding statement: the study was partially funded by Biofire Diagnostics and BioMérieux. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

CMA reports research grants to her institution from Qiagen, Biofire Diagnostics, Pfizer, Roche Diagnostics, BioMérieux, Alere and Genomica SAU, and compensation fees from Qiagen, Roche Diagnostics and BioMérieux for scientific presentations in satellite symposiums; PB reports compensation fees from Roche Diagnostics for scientific presentations in satellite symposiums. The rest of authors report no conflict of interest.