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Rapid PCR for Pneumonia Pathogen Identification

PCR for Pneumonia Pathogen Identification

Pneumonia patients are frequently overtreated with antibiotics because it is difficult to quickly identify the pathogen responsible for their symptoms. The BIOFIRE® FILMRRAY® Pneumonia (PN) Panel delivers fast, accurate pathogen identification in about an hour, which may allow physicians to put patients on appropriate therapy quicker.

Person examines x-ray of chest

Lower respiratory tract infections are a leading cause of morbidity and mortality in the US and worldwide.1,2 Ideally, antimicrobial therapy would be pathogen-specific and guided by the results of microbiology tests. However, current microbiologic methods are slow and fail to identify a causative pathogen in over 60% of patients.3 As a result, patients are often treated empirically, which leads to overuse of broad-spectrum antibiotics.

There is an urgent need for improved diagnostics for lower respiratory tract infections. One promising new diagnostic tool is the BIOFIRE® FILMARRAY® Pneumonia (PN) Panel. The BIOFIRE PN Panel was FDA cleared in 2018 for the detection of 33 clinically relevant targets—including fifteen typical bacteria, three atypical bacteria, eight viruses, and seven antibiotic resistance genes—directly from sputum and bronchoalveolar lavage (BAL) specimens. The test takes about two minutes of hands-on time and delivers results in about an hour. Semi-quantitative information is provided for the fifteen typical bacteria, which may provide additional guidance in patient management.

Initial comparisons with standard methods show good overall concordance. However, the BIOFIRE PN Panel detects more pathogens, primarily driven by increased test sensitivity due to the detection of nucleic acid instead of live organism. In a comparison of pathogen detection by conventional testing (bacterial culture and clinician directed molecular testing for viruses and atypical bacteria) versus the BIOFIRE PN Panel, at least one bacterial pathogen was identified by both methods for 23% of BALs and 35% of sputum samples.4,5 At least one bacterial pathogen was identified by both methods for 23% of BALs and 35% of sputum samples.5 But the BIOFIRE PN Panel detected bacterial pathogens in an additional 15% of BAL samples and 21% of the sputum samples.4,5

Reviews showed that many patients with additional detections had been pretreated with antibiotics (50%) or had cultures with normal oral flora reported (49%).4 In addition, results can be available within a few hours instead of the days required for culture results. One study estimated a reduction in time to result of about 42 hours.6 It is important to note that while the BIOFIRE PN Panel has higher detection rates for the organisms with assays on the panel, the panel does not have assays for all possible bacterial pathogens and should be used in conjunction with culture.

The ability of the BIOFIRE PN Panel to impact patient management, including the ability to change antimicrobial therapy, has also been evaluated. Two groups found that use of the BIOFIRE PN Panel could lead to antibiotic de-escalation in about 50% of patients, with the most common being discontinuation of vancomycin (35%) and piperacillin/tazobactam (23%).4,7

A group in the UK evaluated 120 ICU patients using the results of the BIOFIRE PN Panel.8 Patients were divided into those with positive outcomes (pneumonia resolved) and negative outcomes (pneumonia not resolved in 21 days or contributed to the patient's death). Empiric antibiotic regimens were assessed to be "active" or "inactive" against organisms detected by the BIOFIRE PN Panel and routine culture. In both groups, the BIOFIRE PN Panel would lead to better antimicrobial therapy, which may improve patient outcomes.8

In summary, lower respiratory tract infections are a common and serious healthcare problem, and there is an urgent need for improved diagnostics to guide targeted therapy. While there is still a lot to learn about the optimal use and interpretation of molecular assays, early theoretical outcomes evaluations provide reason to be optimistic.

References

  1. GBD 2015 LRI Collaborators. Lancet Infect Dis. 2017;17:1133-61.
  2. Kochanek D, et al. Nat Vital Stat Rep 2019;68:9.
  3. Jain S, et al. NEJM. 2015;373(5):415-27.
  4. Buchan B, et al. J Clin Microbiol. 2020;58(7):e00135-20.
  5. Faron M, et al. ASM 2018 poster.
  6. Webber D, et al. J Clin Microbiol. 2020;58(7):e00343-20.
  7. D DeBoer S, et al. CVS 2019 poster.
  8. Enne V, et al. ECCMID 2019 poster.

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