Table 2:
Established respiratory pathogens detected by culture, PCR, or mNGS.
| Upper respiratory PCR or lower respiratory culture | Lower respiratory mNGS | PCR or culture, or mNGS, or both | Co-detected (% of cases)* | |
|---|---|---|---|---|
|
| ||||
| Patients | 276 | 276 | 276 | ·· |
| Any positive | 184 (67%) | 249 (90%) | 255 (92%) | ·· |
| Respiratory syncytial virus | 113 (41%) | 116 (42%) | 127 (46%) | 108/127 (85%) |
| Haemophilus influenzae | 29 (1‘%) | 65 (24%) | 70 (25%) | 67/70 (96%) |
| Moraxella catarrhalis | 36 (13%) | 48 (17%) | 65 (24%) | 57/65 (88%) |
| Rhinovirus (A, B, C) | 12 (4%) | 57 (21%) | 61 (22%) | 41/61 (67%) |
| Streptococcus pneumoniae | 19 (7%) | 20 (7%) | 32 (12%) | 30/32 (94%) |
| Staphylococcus aureus | 21 (8%) | 7 (3%) | 25 (9%) | 22/25 (88%) |
| Parainfluenza virus (1–4) | 15 (5%) | 16 (6%) | 22 (8%) | 19/22 (86%) |
| Adenovirus | 19 (7%) | 3 (1%) | 20 (7%) | 20/20 (100%) |
| Coronavirus (HCoV-229E, HCoV-NL63, HCoV-OC4) | 16 (6%) | 9 (3%) | 18 (7%) | 18/18 (100%) |
| Human metapneumovirus | 10 (4%) | 17 (6%) | 17 (6%) | 15/17 (88%) |
| Influenza virus (A, B, C) | 8 (3%) | 9 (3%) | 11 (4%) | 9/11 (82%) |
| Escherichia coli | 6 (2%) | 3 (1%) | 9 (3%) | 8/9 (89%) |
| Human bocavirus | 0 | 9 (3%) | 9 (3%) | 4/9 (44%) |
| Pseudomonas aeruginosa | 5 (2%) | 7 (3%) | 9 (3%) | 8/9 (89%) |
| Viridans streptococci | 6 (2%) | 1 (<1%) | 7 (3%) | 7/7 (100%) |
| Human herpesvirus 6 or 7 | 0 | 5 (1·8%) | 5 (2%) | 5/5 (100%) |
| β-haemolytic streptococcus | 3 (1%) | 2 (1%) | 5 (2%) | 5/5 (100%) |
| Klebsiella pneumoniae | 3 (1%) | 0 | 3 (1%) | 3/3 (100%) |
| Pneumocystis jirovecii | 0 | 3 (1%) | 3 (1%) | 2/3 (67%) |
| Serratia marcescens | 3 (1%) | 0 | 3 (1%) | 3/3 (100%) |
| Enterobacter sp | 1 (<1%) | 1 (<1%) | 2 (1%) | 2/2 (100%) |
| Fusobacterium nucleatum | 0 | 2 (1%) | 2 (1%) | 2/2 (100%) |
| Mycoplasma pneumoniae | 0 | 2 (1%) | 2 (1%) | 0/2 (0%) |
| Parechovirus | 0 | 2 (1%) | 2 (1%) | 2/2 (100%) |
| Bordetella pertussis | 1 (<1%) | 1 (<1%) | 1 (<1%) | 1/1 (100%) |
| Citrobacter freundii | 1 (<1%) | 0 | 1 (<1%) | 1/1 (100%) |
| Morganella morganii | 0 | 1 (<1%) | 1 (<1%) | 1/1 (100%) |
| Stenotrophomonas maltophilia | 1 (<1%) | 1 (<1%) | 1 (<1%) | 1/1 (100%) |
Data are n, n (%), or n/N (%). Patients with definite LRTI had both a clinical diagnosis of LRTI or pneumonia and a microbiological diagnosis made using clinician-ordered culture and PCR-based diagnostic testing. Patients with suspected LRTI had only a clinical diagnosis of LRTI or pneumonia with negative clinician-ordered microbiologic testing. LRTI=lower respiratory tract infection. mNGS=metagenomic next generation sequencing.
*
Co-detected refers to a microbe that was detected along with other microbes in a patient, including multiple viruses or multiple bacteria.