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

Dagfinn Lunde Markussen*, Marit Ebbesen, Sondre Serigstad, Siri Tandberg Knoop, Christian Ritz, Rune Bjørneklett, Øyvind Kommedal, Synne Jenum, Elling Ulvestad, Harleen M.S. Grewal*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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 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.

Original languageEnglish
JournalMicrobiology Spectrum
Issue number5
Number of pages14
Publication statusPublished - Oct 2023


  • diagnostics
  • filmarray
  • gram stain
  • microcopy
  • molecular methods
  • pneumonia
  • quality assurance
  • rapid tests
  • sputum
  • syndromic PCR


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