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Test Code LAB10012 Pneumonia PCR with aerobic culture and Gram stain

Performing Laboratory

Barnes-Jewish Hospital Molecular Infectious Disease (PCR) and Microbiology (aerobic culture and Gram stain) Laboratories

Methodology

Multiplex Polymerase chain reaction (PCR) with corresponding aerobic culture and Gram stain.

The Pneumonia Panel PCR detects viral and bacterial causes of pneumonia (Table 1).  Viral pathogens will be reported qualitatively (i.e. “detected” or “not detected”).  The bacterial targets will be reported in semi-quantitative bins (i.e. 10^4, 10^5, 10^6 and ≥10^7 copies/mL).  Some molecular markers of antimicrobial resistance will also be available for the bacterial targets.  When compared to culture, the pneumonia panel has shown high sensitivity for bacterial targets, with an excellent negative predictive value for on-panel targets.

Table 1.  BioFire Pneumonia Panel Targets

 

 

 

 

Viruses

Adenovirus

Coronavirus (not SARS-CoV-2)

Human metapneumovirus

Human rhinovirus/enterovirus

Influenza A

Influenza B

Parainfluenza virus

Respiratory syncytial virus

 

 

 

 

 

 

 

 

Bacteria (reported with semi-quantification)

Acinetobacter calcoaceticus-baumannii complex

Enterobacter cloacae complex

Escherichia coli

Haemophilus influenzae

Enterobacter aerogenes

Klebsiella oxytoca

Klebsiella pneumoniae group

Moraxella catarrhalis

Proteus spp.

Pseudomonas aeruginosa

Serratia marscens

Staphylococcus aureus

Streptococcus agalactiae

Streptococcus pneumoniae

Streptococcus pyogenes

 

Atypical Bacteria (not quantified)

Chlamydia pneumoniae

Mycoplasma pneumoniae

Legionella pneumophila

 

 

 

Antimicrobial Resistance Genes

mecA/C and MREJ (S. aureus)

blaoxa-48 (Enterobacterales)

blavim  (Enterobacterales)

blaimp  (Enterobacterales)

blakpc  (Enterobacterales)

blaNDM-1  (Enterobacterales)

blaCTX-M  (Enterobacterales)

 

 

NOTE: While the Pneumonia panel PCR detects seasonal coronaviruses, it does not detect SARS-CoV-2 (COVID-19). 

Literature References:

Webber DM, Wallace MA, Burnham CA, Anderson NW. Evaluation of the BioFire FilmArray Pneumonia Panel for Detection of Viral and Bacterial Pathogens in Lower Respiratory Tract Specimens in the Setting of a Tertiary Care Academic Medical Center. JCM 2020 Jun 24;58(7):e00343-20

Hughes AEO, Webber DM, Wallace MA, Johnson C, Burnham CA, Anderson NW. Comparable Detections of Viral Pathogens in Lower Respiratory Tract Specimens with the BioFire Respiratory Panel 2 and the BioFire Pneumonia Panel

Specimen Requirements

Acceptable Specimens:

Sputum, tracheal aspirates, bronchial washing, bronchial alveolar lavage

 Collection Procedure:

  1. Aseptically collect > 1 mL of specimen.
  2. Place in a leakproof screw-capped, sterile container.
  3. Maintain sterility and forward to laboratory promptly

Unacceptable specimens:

Nasopharyngeal swab, nasal swab, saliva

Day(s) Test Set Up

Monday – Sunday, 24 hours

Turnaround Time: 8 hours

Test Classification and CPT Coding

87633 – Respiratory virus multiplex, 12-25 targets

87070 – Culture, aerobic (not stool, rectal swab, or urine)

87205 – Gram stain

87181 – Susceptibility, agar diffusion (if appropriate)

87184 – Susceptibility, disk diffusion (if appropriate)

84185 – Susceptibility, enzyme detection (if appropriate)

87186 – Susceptibility, microdilution (if appropriate)

Reference Values

Not Detected

Test Limitations

Qualitative and quantitative results may differ from those obtained by culture. Final interpretation of Pneumonia Panel results should be in context with results obtained from culture.

While the Pneumonia panel PCR detects seasonal coronaviruses, it does not detect SARS-CoV-2 (COVID-19). 

Specimen Transport Temperature

Specimens should be forwarded to the laboratory immediately for testing.

If immediate forwarding is not possible, specimens should be refrigerated at 2-8˚C.

Refrigerated specimens must be tested within 24 hours.

Requests to add on Pneumonia PCR to existing respiratory culture must be received within 8 hours of culture start. otherwise a new sample will be requested.

Additional Information

For BJH Laboratory Use Only

Minimum Volume:  0.5 mL