Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections

Figures & data

Table 1. Targets of the Biofire pneumonia panel plus.

Bacteria (semi-quantitative)

Acinetobacter calcoaceticus-baumannii complex

Enterobacter cloacae complex

Escherichia coli

Haemophilus influenzae

Klebsiella aerogenes

Klebsiella oxytoca

Klebsiella pneumoniae group

Moraxella catarrhalis

Proteus spp.

Pseudomonas aeruginosa

Serratia marcescens

Staphylococcus aureus

Streptococcus agalactiae

Streptococcus pneumoniae

Streptococcus pyogenes

Atypical bacteria (qualitative)

Legionella pneumophila

Mycoplasma pneumoniae

Chlamydia pneumoniae

Viruses

Influenza A

Influenza B

Adenovirus

Coronavirus

Parainfluenza virus

Respiratory Syncytial virus

Human Rhinovirus/Enterovirus

Human Metapneumovirus

MERS-CoV

Antimicrobial resistance genes

CTX-M

KPC

NDM

Oxa48-like

VIM

IMP

mecA/mecC and MREJ

Figure 1. Schematic algorithm for assessment empirical treatment coverage and supposed impact on isolation practices in relation to the Biofire pneumonia panel plus (BP) results.

Table 2. Descriptive data of enrolled patients.

	Male	Female	Total
Total No (%)	49 (58)	35 (42)	84
Age Median (range)	67 (6–92)	62 (12–89)	65 (6–92)
Clinic No
Intensive care unit	19	2	21
Infectious diseases	3	9	12
Internal medicine	8	8	16
Chest	9	10	19
Pediatrics	2	2	4
Other	8	4	12
Preliminary diagnosis from referral No (%)
Community-acquired pneumonia	16 (33)	13 (37)	29 (35)
Ventilator-associated pneumonia	3 (6)	0 (0)	3 (4)
Hospital-acquired pneumonia	2 (4)	0 (0)	2 (2)
Acute exacerbation of chronic lung disease	4 (8)	10 (29)	14 (17)
Lower respiratory tract infection, unspecified	24 (49)	12 (34)	36 (43)
Sample type
Sputum	30	29	59
Trach aspirate	7	2	9
Broncho-alveolar lavage	12	4	16
Aetiology identified No (%)
Standard diagnostics	30 (61)	20 (57)	50 (60)
BP panel plus standard diagnostics	32 (65)	29 (83)	61 (73)
>1 pathogen	18 (37)	19 (54)	37 (44)
Info about antimicrobial therapy available No (%)	26 (53)	18 (51)	44 (52)

BP: Biofire Pneumonia panel plus.

Table 3. Summary of findings from the Biofire Pneumonia panel plus (BP) and standard diagnostic methods.

Pathogen	No samples analysed by standard method	Total No findings	Unique findings by BP panel	Unique findings by standard methods
Acinetobacter	79	0	0	0
E. cloacae	79	1	1	0
E. coli	79	4	0	0
H. influenzae	79	22	6	1
K. aerogenes	79	0	0	0
K. oxytoca	79	1	0	0
K. pneumoniae	79	1	0	0
M. catarrhalis	79	5	3	0
Proteus spp.	79	0	0	0
P. aeruginosa	79	6	2	0
S. marcescens	79	1	0	0
S. aureus	79	13	9	0
S. agalactiae	79	3	2	1
S. pneumoniae	79	8	2	0
S. pyogenes	79	2	1	0
L. pneumophila	7	1	0	0
M. pneumoniae	9	3	1	0
C. pneumoniae	9	0	0	0
Influenza A	9	0	0	0
Influenza B	9	0	0	0
Adenovirus	18	4	3	0
Coronavirus	18	2	2	0
PIV	18	3	0	0
RSV	9	1	1	0
Rhino/Entero	18	18	12	0
Metapneumo virus	9	0	0	0
MERS-CoV	18	0	0	0

84 samples were analysed by the BP panel for all pathogens. The number of samples analysed by standard methods vary dependent on the requests of the referring clinician.

Table 4. Comparison of the Biofire pneumonia panel plus (BP) to standard methods.

Test	SM + BP +	SM + BP −	SM −BP +	SM −BP −	PPA (95% CI)	NPA (95% CI)	PPV (95% CI)	NPV (95% CI)
BP panel overall	43	7	11	23	86.0 (73.8–93.1)	67.7 (50.8–80.9)	77.6 (79.6–88.2)	76.7 (59.1–88.2)
BP panel, in-panel targets only	43	0	11	30	100 (91.8–100)	73.2 (58.1–84.3)	79.6 (67.1–88.2)	100 (88.7–100)
BP panel, AMR-genes	3	0	0	81	100 (43.9–100)	100 (95.5–100)	100 (43.9–100)	100 (95.5–100)

Identification of any aetiology or resistance gene in lower respiratory samples. SM: Standard method. BP: Biofire pneumonia panel plus; PPA: Positive percent agreement; NPA: Negative percent agreement; PPV: Positive predictive value; NPV: Negative predictive value.

Figure 2. Comparison between the concentrations reported from culture diagnostics (CFU/ml) and the semi-quantitative results from the Biofire Pneumonia panel plus (BP), (DNA copies/ml). The figure shows all 33 results where a semi-quantitative result, above cut-off, was available from both methods for the same target.