Figure 1.
Figure 2.
Figure 3.
Targets of the BioFire pneumonia panel
| Bacteria | Atypical bacteria | Viruses | Antimicrobial resistance genes |
|---|---|---|---|
| Strept_agalactiae | Chlamydia_P | Adenovirus | IMP |
| Strept Pneumoniae | Legionella_P | Coronavirus | KPC |
| Strept_Pyogenes | Mycoplasma_P | Human_Metapneumovirus | mecA_C_and_MREJ |
| Moraxella_catarrhalis | Human_Rhinovirus_Enterovirus | NDM | |
| Proteus | INFLUENZA_B | OXA_48_like | |
| Pseudomonas aeruginosa | INFLUENZA_A | VIM | |
| Serratia_marcescens | MERS_CoV | IMP | |
| Staph_aureus | Parainfluenza | KPC | |
| E._Coli | RSV | IMP | |
| H_influenzae | |||
| Klebsiella_aerogenes | |||
| Klebsiella_oxytoca | |||
| Klebsiella_Pneumoniae | |||
| Acinetobacter calcoaceticus baumannii_complec | |||
| Enterobacter cloacae complex |
Qualitative detection of bacterial targets between the BioFire PN Panel and SOC culture
| Specimens (no of BFPP detections/no of standard culture detections) | |||||||
|---|---|---|---|---|---|---|---|
| (+/+) True Positive | (±) False Positive | (-/+) False Negative | (-/-) True Negative | PPA%. [95% CI] | NPA%. [95% CI] | OPA%. [95% CI] | |
| Strept_agalactiae | 0 | 13 | 0 | 223 | NA | 94.49 [90.76–97.03] | 94.51 [90.76–97.03] |
| Strept Pneumoniae | 1 | 7 | 0 | 228 | 99.58 [97.64–99.98] | 97.02 [93.96–98.79] | 97.03 [93.98–98.80] |
| Strept_Pyogenes | 0 | 1 | 0 | 235 | NA | 99.58 [97.66–99.99] | 99.58 [97.67–99.99] |
| Moraxella_catarrhalis | 0 | 2 | 0 | 234 | NA | 99.15 [96.97–99.90] | 97.05 [94.01–98.80] |
| Proteus | 1 | 6 | 0 | 229 | 99.58 [97.64–99.98] | 97.41 [94.46–99.05] | 97.5 [94.48–99.1] |
| Pseudomonas aeruginosa | 21 | 28 | 4 | 183 | 89.41 [84.83–92.72] | 86.7 [73.61–83.92] | 86.44 [81.40–90.54] |
| Serratia_marcescens | 0 | 7 | 0 | 229 | 100 [98.40–100.0] | 97.03 [93.98–98.80] | 97.05 [94.01–98.80] |
| Staph_aureus | 10 | 22 | 0 | 204 | 95.76 [92.38–97.68] | 90.3 [85.63–93.80] | 90.68 [86.23–94.07] |
| E._Coli | 22 | 21 | 3 | 190 | 88 [84.83–92.72] | 90.05 [85.19–93.73] | 89.83 [85.25–93.37] |
| H_influenzae | 1 | 6 | 0 | 229 | 99.58 [97.64–99.98] | 97.45 [94.53–99.06] | 97.46 [94.55–99.06] |
| Klebsiella_aerogenes | 0 | 5 | 0 | 231 | 100 [98.40–100.0] | 97.88 [95.13–99.31] | 97.89 [95.15–99.31] |
| Klebsiella_oxytoca | 1 | 4 | 0 | 231 | 99.58 [97.64–99.98] | 98.30 [95.70–99.53] | 98.31 [95.72–99.54] |
| Klebsiella_pneumoniae | 36 | 25 | 13 | 162 | 73.47 [58.92–85.05] | 86.63 [80.90–91.16] | 83.90 [78.58–88.35] |
| Acinetobacter calcoaceticus baumannii_complec | 7 | 20 | 2 | 207 | 96.19 [92.91–97.98] | 91.2 [83.87–92.02] | 90.68 [86.23–94.07] |
| Enterobacter cloacae complex | 1 | 16 | 0 | 219 | 99.58 [97.64–99.98] | 93.19 [89.18–96.06] | 93.22 [89.22–96.08] |
| Total bacterial pathogens | 100 | 177 | 22 | 3,006 | 81.97 [73.98–88.34] | 94.44 [93.59–95.21] | 93.98 [93.11–94.77] |
Characteristic data of participating subjects
| Mean | SD | ||
|---|---|---|---|
| Age (years) | 62.89 | 18.61 | |
| Age category (F/%) | |||
| 18–35 (years) | 33 | 14.0 | |
| 36–50 (years) | 31 | 13.1 | |
| 51–65 (years) | 42 | 17.8 | |
| >65 (years) | 130 | 55.1 | |
| Sex (F/%) | Male | 150 | 63.6 |
| Female | 86 | 36.4 | |
| Smoking status (F/%) | |||
| Current smoker | 140 | 59.3 | |
| Ex-smoker | 16 | 6.8 | |
| Non-smoker | 80 | 33.9 | |
| SI (Pack.year) | 17.94 | 18.36 | |
| Comorbidities (F/%) | |||
| DM | 127 | 53.81 | |
| HTN | 110 | 46.6 | |
| IHD | 85 | 36.0 | |
| Chr_Resp_Dis | 37 | 15.68 | |
| CKD | 36 | 15.25 | |
| Others | 55 | 23.3 | |
| Antimicrobial use before hospitalisation (F/%) | 184 | 77.96 | |
| Hosp_LOS (days) | 23.49 | 32.32 | |
| ICU_LOS (days) | 16.95 | 21.91 | |
| MV_Dur (days) | 5.95 | 14.82 | |
| Outcome (F/%) | Discharged | 176 | 74.6 |
| In-hospital mortality | 60 | 25.4 | |
| 30-day mortality (F/%) | 43 | 18.22 | |
Frequency and percentage of resistance genes
| Frequency | Percent (%) | ||
|---|---|---|---|
| Carbapenemase producing Gram negative bacilli | VIM | 9 | 3.81 |
| IMP | 2 | 0.85 | |
| KPC | 2 | 0.85 | |
| NDM | 60 | 25.42 | |
| OXA-48 like | 42 | 17.8 | |
| Total carbapenamase producers | 115 | 48.73 | |
| ESBL producing bacteria | CTX_M | 75 | 31.78 |
| Methicillin resistant Staphylococcus aureus | mecA_C_and_MREJ | 24 | 10.17 |
| Total | 214 | 90.68 |
Comorbid disease association with resistance genes
| DM | HTN | IHD | Chronic respiratory disease | CKD | Others | |
|---|---|---|---|---|---|---|
| VIM | 2.4 | 2.5 | 2.4 | 8.1 | 2.8 | 1.8 |
| IMP | 1.6 | 0.4 | 1.2 | 0 | 0 | 1.8 |
| KPC | 0 | 0 | 0 | 2.7 | 0 | 0 |
| mecA_C_and_MREJ | 7.1 | 3.8 | 10.6 | 10.8 | 2.8 | 10.9 |
| NDM | 22.8 | 14 | 34.1 | 24.3 | 33.3 | 30.9 |
| OXA_48_like | 14.2 | 6.8 | 22.4 | 13.5 | 22.2 | 20 |
| CTX_M | 27.6 | 13.6 | 34.1 | 27 | 27.8 | 34.5 |
Comorbid disease association with infecting organisms
| DM | Chronic respiratory disease | CKD | HTN | IHD | Other diseases | |
|---|---|---|---|---|---|---|
| Klebsiella pneumoniae | 22 | 21.6 | 30.6 | 10.2 | 28.2 | 25.5 |
| Pseudomonas aeronginosa | 18.9 | 35.1 | 13.9 | 11.4 | 20 | 29.1 |
| E. coli | 11.8 | 10.8 | 30.6 | 5.1 | 20 | 14.5 |
| Acinetobacter baumannii | 13.4 | 5.4 | 16.7 | 8.9 | 20 | 16.4 |
| Enterobacter_cloacae_complex | 4.7 | 10.8 | 11.1 | 3 | 7.1 | 9.1 |
| Staphylococcus aureus | 11 | 21 | 5.6 | 5.1 | 15.3 | 18.2 |
| BF_Strept_agalactiae | 7.1 | 8.1 | 8.3 | 2.1 | 4.7 | 5.5 |
| BF_Strept_P | 3.9 | 2.7 | 5.6 | 1.7 | 3.5 | 1.8 |
| BF_Strept_Pyogenes | 0 | 0 | 0 | 0 | 0 | 0 |
| BF_Moraxella_catarrhalis | 0.8 | 0 | 2.8 | 0.8 | 2.4 | 1.8 |
| BF_Proteus | 2.4 | 5.4 | 8.3 | 0.8 | 5.9 | 1.8 |
| BF_Serratia_marcescens | 3.9 | 5.4 | 0 | 1.7 | 4.7 | 1.8 |
| BF_H_influenzae | 4.7 | 2.7 | 2.8 | 2.1 | 2.4 | 1.8 |
| BF_Klebsiella_aerogenes | 0.8 | 8.1 | 11.1 | 0.4 | 2.4 | 3.6 |
| BF_Klebsiella_oxytoca | 2.4 | 5.4 | 2.8 | 0.4 | 3.5 | 1.8 |