Guidance on Use of the Pneumonia Panel for Respiratory Infections
Although the number of pathogens that cause pneumonia is lengthy, establishing the microbiologic etiology of
pneumonia is inherently difficult. A recent large multi-center study of community-acquired pneumonia (CAP)
found that only 38% of 2259 CAP cases had a microbiologic diagnosis with 23% having viruses detected, 11%
bacterial, and 3% had both viruses and bacteria detected.
1
Current tools to assist in pneumonia diagnosis include
respiratory tract cultures (sputum, BAL, tracheal aspirate, mini-BAL), urine antigens (pneumococcal, Legionella),
serology, and PCR for viral and certain bacterial pathogens. While these tools are useful, the study noted above
used all these tools and was unable to document an etiology causing pneumonia in 62% of patients. Thus, more
sensitive tools for detection of respiratory pathogens are still needed.
Nebraska Medicine has recently introduced a new FDA-approved multiplex PCR panel to assist in determination
of the etiology of pneumonia, termed the Pneumonia Panel (PP). This test uses a nested multiplex PCR-
approach to amplify nucleic acid targets directly from sputum or bronchoalveolar lavage (BAL) in patients with
suspected pneumonia. The list of pathogens and resistance genes included in the panel is found in Table 1.
Note that the bacterial targets are detected semi-quantitatively whereas the atypical pathogens and the viral
targets are detected qualitatively.
Table 1: Pneumonia Panel Pathogen Targets and Associated Resistance Genes
Semi-quantitative Detection:
Gram Positive Organisms:
Staphylococcus aureus
Streptococcus pneumoniae
Streptococcus agalactiae
Streptococcus pyogenes
Resistance Genes (Staph aureus only):
mecA/C and MREJ
Gram Negative Organisms:
Acinetobacter calcoaceticus-baumannii complex
Enterobacter cloacae complex
E. coli
Haemophilus influenzae
Klebsiella aerogenes
Klebsiella oxytoca
Klebsiella pneumonia
Moraxella catarrhalis
Proteus spp.
Pseuodomonas aeruginosa
Serratia marcescens
Resistance Genes (All Gram Negatives):
CTX-M
IMP
KPC
NDM
VIM
OXA-48-like
Qualitative Detection:
Atypical Pathogens:
Chlamydia pneumoniae
Legionella pneumophila
Myocplasma pneumoniae
Viral Pathogens:
Adenovirus
Coronavirus
Human Metapneumovirus
Rhinovirus/Enterovirus
Influenza A
Influenza B
Parainfluenza
RSV
Pneumonia Diagnostic Issues:
The diagnosis of pneumonia is difficult as many other conditions can mimic pneumonia such as heart failure,
pleural effusion, malignancy, etc. Thus, the Pneumonia Panel should only be ordered in patients with a clinical
syndrome highly suggestive of pneumonia. It should not be used to decide if a patient has pneumonia. Patients
can be colonized with organisms that are detected by the panel even when pneumonia is not present. Therefore
a positive result on the pneumonia panel does not mean the patient has pneumonia or that antibiotics should
be started. The decision to start antibiotics should be a clinical decision, while the panel should be used to
refine and adjust the use of antibiotics, not to decide whether they are needed. Biomarkers such as
procalcitonin can be helpful in determining if antibiotics are indicated (see guidance on ASP website).
Respiratory Tract Cultures:
All specimens submitted for Pneumonia Panel testing will simultaneously be cultured. If a sputum is obtained
and judged to be of poor quality based on Gram stain (>25 squamous cells/hpf) it will be rejected and a new
specimen should be obtained. Complete culture results are generally reported within 48-72 hours.
Criteria for Pneumonia Panel Use: This test should only be used in patients who have clear evidence of
pneumonia (signs and symptoms + increased oxygen need + new or progressive radiographic infiltrate). Use
should be restricted to situations where the result will change therapy. Recent CAP guidelines suggest that
clinicians should not use diagnostic testing in patients with non-severe CAP being treated with typical therapy
(see ASP pneumonia guidelines).
2
The Pneumonia Panel should be considered in the following situations:
1) Patients with severe CAP (admitted to ICU, respiratory failure, etc.).
2) CAP patients on expanded-spectrum therapy (vancomycin, cefepime, etc.).
3) Patients not responding to typical therapy.
4) Patients with hospital-acquired or ventilator-associated pneumonia.
Pneumonia panel ordering is restricted to the ICU or the Infectious Disease and Pulmonary team. If a sputum
test was performed, the panel may be ordered on a subsequent BAL specimen, independent of the time
between specimens’ collection. Otherwise, the Pneumonia panel cannot be repeated within 10 days unless
discussed with the microbiology director.
Issues with Interpretation:
Respiratory Tract Colonization: The interpretation of results from this panel are complicated by a number of
issues. First, various organisms may colonize the respiratory tract without causing infection. For example, S.
aureus or S. pneumoniae often colonize the nasopharynx whereas Pseudomonas aeruginosa often colonizes the
lower respiratory tract, particularly in the setting of structural lung disease. Sputum and BAL are therefore not
expected to be sterile. The highly sensitive nature of nucleic acid testing means that the Pneumonia Panel may
detect colonizing organisms that would not be detected in culture or that would be reported as “normal
respiratory flora” due to their limited quantity. Treatment decisions should be based on the clinical likelihood of
pneumonia, not necessarily on the detection of organisms.
Multiple Organism Detection: Patients may have more than one organism detected in their sputum or BAL. In
the validation study of the pneumonia panel, 38% of 413 positive BAL specimens and 56% of 602 positive
sputum specimens had >1 organism detected. Combinations of both viruses and bacteria and multiple bacteria
were found. BAL specimens were more likely to be mono-microbial than sputum. When multiple organisms
were present, the most abundant organism detected by the Pneumonia Panel was usually the most prevalent
organism detected by culture (concordance 79% BAL, 86% sputum). Most bacterial pulmonary infections are
monomicrobial in nature and generally only the most common bacterial pathogen should be targeted for
antibacterial therapy.
Positive Panel with a Negative Culture: Molecular tests are more sensitive than traditional culture methods for
the detection of bacterial organisms and the panel may detect organisms at very low levels. In validation
testing, the pneumonia panel found at least one organism in 49% of BAL specimens and 72% of sputum
specimens. The sensitivity was determined using quantitative culture confirmed in culture negative specimens
using additional molecular tests. The results of this analysis is included below in Table 3. Overall the panel is
very sensitive for the detection of most respiratory tract pathogens. Organisms detected by the panel that were
not found in quantitative culture were frequently present at levels below what quantitative culture could detect
or were only detected using other molecular methods. This may be because the organisms were in very low
levels or were non-viable due to antibiotic pre-treatment. This occurred most frequently with S. aureus, H.
influenzae, and P. aeruginosa. The pneumonia panel will always be accompanied by a clinical culture to confirm
the presence of bacterial pathogens and determine antimicrobial susceptibility. Interpretation of positive panel
result with a negative culture requires clinical consideration. Organisms such as S. aureus and P. aeruginosa are
relatively easy to detect using routine cultures, while other organisms such as H. influenzae and S. pneumoniae
are more difficult to detect, particularly after antibiotics have been started. With this in mind if S. aureus
(especially MRSA) and/or P. aeruginosa are detected by the panel but not confirmed by culture, therapy
directed at these organisms can be de-escalated to typical community-acquired pneumonia coverage. This is in
line with current HAP/VAP guidelines, which recommend that when organisms are not detected in culture,
therapy should be withheld or discontinued.
3
Bin Number Interpretation: Bacterial pathogens will be reported as either Not Detected or semi-quantitatively
via a “Bin.” These Bin’s represent the relative abundance of nucleic acid in the specimen and are reported as
copies/mL. The Bin numbers do not correlate with quantitative cultures and are usually higher than what would
be detected on quantitative culture. Samples with Bin numbers of 10
4
or 10
5
, particularly with S. aureus, H.
influenzae and Pseudomonas aeruginosa may not be detected in culture. Thus, with certain pathogens, such as
S. aureus, Bin numbers of 10
4
or 10
5
may reflect colonization particularly from an expectorated sputum sample.
Viral and atypical pathogens and resistance gene markers are reported qualitatively as Detected or Not
Detected.
Antimicrobial Resistance Gene Markers:
• mecA encodes for PBP2A and functions to mediate methicillin (oxacillin) resistance in S. aureus. A
positive result for mecA suggests that MRSA is present. A negative result for mecA suggests that the S.
aureus is susceptible to semi-synthetic penicillins, -lactam/ -lactamase inhibitor combinations or
cefazolin/ceftriaxone and typical CAP therapy can be continued.
• CTX-M (bla
CTX-M
) encodes for the most common extended-spectrum -lactamase (ESBL) enzyme found in
gram negative Enterobacteriaceae such as E. coli, Klebsiella pneumoniae, and Proteus mirabilis. ESBLs
hydrolyzes expanded spectrum cephalosporins (ceftriaxone, cefepime) and piperacillin/tazobactam. A
positive results suggests that gram negative therapy should usually be escalated to a carbapenem. A
negative result does not exclude the presence of other ESBLs
• IMP, KPC, NDM, OXA-48-like, and VIM are all carbapenemase gene markers in Enterobacteriaceae and
Pseudomonas aeruginosa. Carbapenemases hydrolyze all -lactam antibiotics including the
carbapenems. Detection of these genes should result in immediate consultation with Infectious
Disease. The absence of these markers does not always predict carbapenem susceptibility as other
mechanisms can result in carbapenem resistance, particularly within Pseudomonas aeruginosa.
Table 2: Therapy Recommendations Based on Pneumonia Panel Results
Listed below are the potential results of the pneumonia panel and specific therapy recommendations based
upon Nebraska Medicine-specific antibiogram data (respiratory tract-specific and overall antibiogram). Previous
respiratory culture results and antibiotic allergies should be taken into account when making therapy decisions.
Pathogen Detected
Preferred Therapy
Staphylococcus aureus
Negative S. aureus
mecA/C negative = MSSA
mecA/C positive = MRSA
Stop MRSA therapy if started
Ampicillin/Sulbactam or
Ceftriaxone
Vancomycin or Linezolid
De-escalation Options:
mecA/C negative: Cefuroxime,
Amoxicillin/clavulanate
mecA/C positive: Linezolid,
TMP/SMX
Streptococcus pneumoniae
No concern for CNS infection
Concern for CNS Infection
Penicillin or Ampicillin
Ceftriaxone PLUS Vancomycin
De-escalation Options (non-CNS):
Amoxicillin, Cefuroxime
Streptococcus pyogenes (Group
A Strep) and Streptococcus
agalactiae (Group B Strep)
Penicillin or Ampicillin or
Cefazolin
De-escalation Options:
Amoxicillin, Cephalexin
Acinetobacter calcoaceticus-
baumannii complex
Meropenem +/- amikacin
De-escalation Options:
Levofloxacin 79-94%
Minocycline 82-85%
Enterobacter (Klebsiella)
aerogenes
Cefepime
De-escalation Options:
Levofloxacin 92-100%
TMP/SMX 96-97%
Enterobacter cloacae
Cefepime
De-escalation Options:
Levofloxacin 100%
TMP/SMX 92-94%
E. coli
CTX-M = Possible Extended-
Spectrum Beta-Lactamse (ESBL)
CTX-M Negative: Cetriaxone or
Pip/tazo
CTX-M Positive: Ertapenem or
Meropenem*
De-escalation Options:
CTX-M Negative: Cefdinir
CTX-M Positive: Use culture data,
limited oral options
Haemophilus influenzae
Ampicillin/sulbactam or
Ceftriaxone
De-escalation Options:
Amoxicillin/clavulanate
Cefdinir/Cefuroxime
Klebsiella oxytoca
Ertapenem or Meropenem*
De-escalation Options:
Levofloxacin 87-98%
TMP/SMX 93-94%
Mino/Doxycycline 91-100%
Klebsiella pneumoniae
Ceftriaxone
De-escalation Options:
Amoxicillin/clavulanate 83-91%
Cefdinir 93-97%
TMP/SMX 87-81%
Levofloxacin 97-98%
Moraxella catarrhalis
Ampicillin/sulbactam or
Ceftriaxone
De-escalation Options:
Amoxicillin/clavulanate
Cefdinir/Cefuroxime
Proteus spp
Ceftriaxone
De-escalation Options:
Amoxicillin/clavulanate 87-90%
Cefdinir/Cefuroxime 96-100%
Pseudomonas aeruginosa
Piperacillin/tazobactam
De-escalation Options:
Levofloxacin 64-73%
Serratia marcescens
Cefepime
De-escalation Option:
Levofloxacin 96-98%
TMP/SMP 98-100%
Gram Negative Resistance
Genes:
CTX-M
IMP, KPC, NDM, OXA-48-like,
VIM
Consider carbapenem use
(ertapenem or meropenem)
Consult ID
Chlamydia pneumonia
Mycoplasma pneumoniae
Azithromycin 500mg once, then
250mg X 4 days
Doxycycline X 7 days
Legionella pneumophila
Levofloxacin 750mg daily X 7 days
Azithromycin 500mg daily X 7
days
Influenza A
Influenza B
Oseltamivir 75mg BID X 5 days
Adenovirus
Coronavirus
Human Metapneumovirus
Rhinovirus/Enterovirus
Parainfluenza
RSV
Symptomatic therapy
Table 3: Performance of Pneumonia Panel Compared to Reference Culture or Molecular Testing
4
Sensitivity
Specificity
Organism
Source
TP/(TP+FN)
% (95% CI)
TN(TN+FP)
% (95% IC)
A. calcoaceticus-
baumannii cmplx
BAL
0/0
-
839/846
99.2% (98.3-99.6%)
Sputum
10/11
90.9% (62.3-98.4%)
807/825
97.8% (96.6-98.6%)
E. aerogenes
BAL
6/7
85.7% (48.7-97.4%)
832/839
99.2% (98.3-99.6%)
Sputum
3/4
75% (30.1-95.4%)
823/832
98.9% (98.0-99.4%)
E. cloacae cmplx
BAL
11/12
91.7% (64.6-98.5%)
11/12
98.6% (97.5-99.2%)
Sputum
822/834
91.7% (64.6-98.5%)
803/824
97.5% (96.1-98.3%)
E. coli
BAL
12/12
100% (75.8-100%)
826/834
95.8% (79.8-99.3%)
Sputum
23/24
99.0% (98.1-99.5%)
878/812
96.9%(95.5-97.9%)
H. influenza
BAL
10/10
100% (72.2-100%)
764/836
91.4% (89.3-93.1%)
Sputum
16/18
88.9% (67.2-96.9%)
727/818
88.9% (86.5-90.9%)
K. oxytoca
BAL
2/2
100% (34.2-100%)
835/844
98.9% (98.0-99.4%)
Sputum
9/9
100% (70.1-100%)
817/827
98.8% (97.8-99.3%)
K. pneumoniae grp
BAL
15/15
100% (79.6-100%)
819/831
98.6% (97.5-99.2%)
Sputum
21/23
91.3% (73.2-97.6%)
769/813
94.6% (92.8-95.9%)
M. catarrhalis
BAL
0/0
-
817/846
96.6% (95.1-97.6%)
Sputum
5/5
100% (56.6-100%)
761/831
91.6% (89.5-93.3%)
Proteus spp.
BAL
5/5
100%(56.6-100%)
837/841
99.5% (98.8-99.8%)
Sputum
15/15
100%(79.6-100%)
813/821
99% (98.1-99.5%)
P. aeruginosa
BAL
36/36
100% (90.4-100%)
103/106
95.3% (93.6-96.6%)
Sputum
103/106
97.2% (92.0-99.0%)
673/730
92.2%(90-93.9%)
S. marcescens
BAL
6/6
100% (61.0-100%)
834/840
99.3% (98.5-99.7%)
Sputum
26/27
96.3% (81.7-99.3%)
782/809
96.7% (95.2-97.7%)
S. aureus
BAL
46/47
97.9% (88.9-99.6%)
729/799
91.2% (89.1-93.0%)
Sputum
111/112
99.1% (95.1-99.8%)
631/724
87.2% (84.5-89.4%)
S. agalactiae
BAL
1/1
-
821/845
97.2% (95.8-98.1%)
Sputum
9/9
100% (70.1-100%)
793/827
95.9% (94.3-97.0%)
S. pneumoniae
BAL
5/5
100% (56.6-100%)
817/841
97.1 (95.8-98.1%)
Sputum
16/16
100% (80.6-100%)
785/820
95.7% (94.1-96.9%)
S. pyogenes
BAL
2/2
100% (34.2-100%)
838/844
99.3 (98.5-99.7%)
Sputum
6/6
100% (61.0-100%)
825/830
99.4% (98.6-997%)
Viruses
Adenovirus
BAL
8/8
100% (67.6-100%)
837/837
100% (99.5-100%)
Sputum
13/17
76.5% (52.7-90.4%)
815/817
99.8% (99.1-99.9%)
Coronavirus
BAL
18/21
85.7% (65.4-95.0%)
810/823
98.4% (97.3-99.1%)
Sputum
28/32
87.5% (71.9-95.0%)
796/802
99.3% (98.4-99.7%)
Human
Metapneumovirus
BAL
8/8
100% (67.6-100%)
836/837
99.9% (99.3-100%)
Sputum
20/21
95.2% (77.3-99.2%)
812/813
99.9% (99.3-100%)
Rhino/Enterovirus
BAL
52/54
96.3% (87.5-99.0%)
771/782
98.6% (97.5-99.2%)
Sputum
96/96
100% (96.2-100%)
717/730
98.2% (97.0-99.0%)
Influenza A
BAL
10/10
100% (72.2-100%)
830/833
99.6% (98.9-99.9%)
Sputum
13/13
100% (77.2-100%)
819/822
99.6% (98.9-99.9%)
Influenza B
BAL
5/6
83.3% (43.6-97%)
837/838
99.9% (99.3-100%)
Sputum
12/12
100% (75.8-100%)
921/923
99.8% (99.1-99.9%)
MERS-CoV
BAL
0/0
-
846/846
100% (99.5-100%)
Sputum
0/0
-
836/836
100% (99.5-100%)
Parainfluenza
BAL
16/18
88.9% (67.2-96.9%)
824/826
99.8% (99.1-99.9%)
Sputum
28/29
96.6% (82.8-99.4%)
804/806
99.8% (99.1-99.9%)
RSV
BAL
3/3
100% (43.9-100%)
841/841
100% (99.5-100%)
Sputum
43/43
100% (91.8-100%)
787/791
99.5% (98.7-99.8%)
Atypical Bacteria
C. pneumoniae
BAL
0/0
-
844/845
99.9% (99.3-100%)
Sputum
0/0
-
835/835
100% (99.5-100%)
L. pneumophila
BAL
2/2
100% (34.2-100%)
833/833
100% (99.5-100%)
Sputum
0/1
-
826/826
100% (99.5-100%)
M. pneumoniae
BAL
3/3
100% (43.9-100%)
841/842
99.9% (99.3-100%)
Sputum
7/8
87.5% (52.9-97.8%)
827/827
100% (99.5-100%)
Created by: Trevor Van Schooneveld MD, Erica Stohs MD, Andre Kalil MD, Hannah Creager PhD, Paul Fey, PhD
References:
1. Jain S, et al. Community-acquired Pneumonia Requiring Hospitalization among US Adults. N Engl J Med.
2015;373:415-27.
2. Metlay J, et al. Diagnosis and Treatment of Adults with Community-acquired Pneumonia: An Official
Clinical Practice Guideline of the American Thoracic Society and Infectious Diseases Society of America.
Am J Respir Crit Care Med. 2019;200:e45-67.
3. Kalil AC, et al. Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia:
2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American
Thoracic Society. Clin Infect Dis. 2016;63:e61-111.
4. BioFire Diagnostics. BioFire® FilmArray® Pneumonia Panel Instruction Booklet.
https://www.biofiredx.com/support/documents/#toggle-id-3 Accessed 1/22/20.