Table 2.
NGS analysis and other key laboratory results of patients in the present cohort
| Case no | Gomori methenamine silver staining | NGS | 1,3-β-D-glucan (pg/mL) | Other positive microbiological tests | ||
|---|---|---|---|---|---|---|
| Specimen | tNGS/mNGS | Sequencing result (number of reads) | ||||
| 1 | Negative | BAL | mNGS | Pneumocystis jirovecii (5), Prevotella melaninogenica (81), Veillonella parvula (5), Mycobacterium intracellulare (1) | 201.61 | None |
| 2 | Not done | Sputum | tNGS | Enterobacter cloacae complex (9), P. jirovecii (19), EBV (17,782), CMV (50), HHV-7 (49), Ureaplasma urealyticum (2) | < 37.5 | None |
| 3 | Negative | BAL | tNGS | P. jirovecii (1886) | < 37.5 | None |
| 4 | Negative | BAL | mNGS | Rothia mucilaginosa (45,448), Streptococcus mitis (13,051), Streptococcus pneumoniae (11,961), P. jirovecii (168), HSV-1 (17), Olsenella uli (18,072), P. melaninogenica (8702), Staphylococcus haemolyticus (6259), V. parvula (3530), Parvimonas micra (3037), Corynebacterium simulans (1984), Cryptobacterium curtum (1390), Filifactor alocis (379), Leptotrichia buccalis (329), Corynebacterium striatum (269), Atopobium parvulum (261), Peptostreptococcus anaerobius (152), Clostridioides difficile (136), Actinomyces oris (82) | > 600 | None |
| 5 | Negative | Sputum | tNGS | Tropheryma whipplei (19,095), Haemophilus influenzae (387), Staphylococcus aureus (26), P. jirovecii (14), rhinovirus C (16,789), EBV (7569) | < 37.5 | None |
| 6 | Negative | BAL | tNGS | Candida albicans (27,428), EBV (3357), Enterococcus faecalis (1925), Stenotrophomonas maltophilia (321), P. jirovecii (141), HHV-7 (136), Trichosporon asahii (34) | < 37.5 | None |
| 7 | Negative | BAL | mNGS | S. aureus (3), P. jirovecii (2), Neisseria flavescens (40), Haemophilus parainfluenzae (15), P. melaninogenica (15), R. mucilaginosa (12), Porphyromonas gingivalis (11), Fusobacterium nucleatum (6), Capnocytophaga granulosa (4), Peptostreptococcus stomatis (4), Aggregatibacter segnis (4), F. alocis (4), Treponema denticola (4), Veillonella dispar (4), Streptococcus pseudopneumoniae (3) | < 37.5 | None |
| 8 | Not done | Sputum | tNGS | Chlamydia psittaci (49), Acinetobacter baumannii (177), H. influenzae (33), Pseudomonas aeruginosa (22), S. maltophilia (14), HHV-7 (32), P. jirovecii (11), HHV-6 (6) | Not done | None |
| 9 | Not done | BAL | mNGS | P. jirovecii (830), Streptococcus species (23), R. mucilaginosa (10), Abiotrophia defectiva (7), Granulicatella adiacens (5), Staphylococcus epidermidis (3), Tannerella forsythia (2), Prevotella denticola (1), EBV (1), Torque teno virus (1) | > 600 | None |
| 10 | Positive | BAL | tNGS | P. jirovecii (48,609), EBV (3) | 394.01 | None |
| 11 | Negative | BAL | mNGS | S. aureus (79), C. albicans (1757), P. jirovecii (2), human polyomavirus 5 (4), Mycobacterium chelonae (3), S. haemolyticus (264,865), Lactobacillus rhamnosus (12,454), Mogibacterium timidum (72), Corynebacterium tuberculostearicum (9) | < 37.5 | None |
| 12 | Positive | BAL | tNGS | P. jirovecii (84,000), Bordetella pertussis (1705), rhinovirus A (44) | 49.72 | None |
| 13 | Not done | Sputum | tNGS | Klebsiella pneumoniae (44,975), A. baumannii (15,986), S. maltophilia (11,464), E. faecalis (11,480), EBV (826), P. jirovecii (87), E. cloacae complex (32), HSV-1 (9) | < 37.5 | None |
| 14 | Not done | BAL | mNGS | P. jirovecii (15), P. melaninogenica (1405), R. mucilaginosa (930), Campylobacter concisus (432), Streptococcus infantis (363), Gemella sanguinis (269), Veillonella atypica (189), Eikenella corrodens (123), Actinomyces graevenitzii (115), Solobacterium moorei (104), Capnocytophaga sputigena (101), H. parainfluenzae (83), A. defectiva (66), L. buccalis (54), P. stomatis (51), Oribacterium sinus (45) | < 37.5 | None |
| 15 | Negative | Sputum | tNGS | EBV (1215), HHV-7 (741), P. jirovecii (72) | < 37.5 | None |
| 16 | Negative | BAL | tNGS | P. jirovecii (4476), C. albicans (4447), Legionella pneumophilia (17), HHV-7 (83), CMV (5) | < 37.5 | None |
| Negative | BAL | tNGS | P. jirovecii (322), C. albicans (178), CMV (12), HHV-7 (10) | < 37.5 | None | |
| 17 | Negative | BAL | tNGS | C. albicans (424), P. jirovecii (135), CMV (135), H. influenzae (19), T. whipplei (54), HHV-7 (6) | 61.96 | None |
| 18 | Negative | BAL | tNGS | Rhinovirus (192), P. aeruginosa (278), P. jirovecii (105), S. pneumoniae (5), EBV (7) | 183.52 | Sputum culture: P. aeruginosa |
| 19 | Not done | Sputum | tNGS | P. aeruginosa (40,038), EBV (882), CMV (23), HHV-7 (12), P. jirovecii (7) | < 37.5 | Sputum culture: P. aeruginosa |
| 20 | Not done | Sputum | tNGS | P. aeruginosa (48,178), Mycobacterium kansasii (150), S. maltophilia (603), EBV (274), P. jirovecii (166), CMV (115), C. albicans (27), HHV-7 (19) | < 37.5 | Sputum for AFB smear: positive; sputum culture: P. aeruginosa |
| 21 | Not done | Sputum | tNGS | S. aureus (6472), P. jirovecii (184), HHV-7 (136), Haemophilus haemolyticus (113) | < 37.5 | None |
| 22 | Not done | Sputum | tNGS | Mycobacterium abscessus (3907), H. influenzae (46,294), H. haemolyticus (355), P. jirovecii (212), EBV (129), HSV-1 (97), CMV (32), HHV-7 (30) | Not done | None |
| 23 | Negative | Sputum | tNGS | Influenza virus A (38,696), Aspergillus fumigatus (76), P. jirovecii (1) | < 37.5 | NPS for Influenza A virus RNA: positive |
| 24 | Not done | Sputum | tNGS | K. pneumoniae (54,414), A. baumannii (10,292), E. faecalis (8694), EBV (1517), CMV (93), S. aureus (88), HHV-7 (46), P. jirovecii (13) | Not done | None |
| 25 | Negative | BAL | tNGS | P. jirovecii (172) | < 37.5 | None |
| 26 | Not done | Sputum | tNGS | A. baumannii (173), H. haemolyticus (51), S. aureus (21), P. jirovecii (8) | < 37.5 | None |
| 27 | Negative | BAL | mNGS | Escherichia coli (61,948), K. pneumoniae (1424), E. cloacae complex (3289), P. jirovecii (1104), HSV (1,095,105), EBV (53), HHV-7 (26), HHV-6B (4), S. epidermidis (494,451), V. parvula (215,980), Actinomyces dentalis (22,892), S. infantis (46,135), Campylobacter curvus (32,006), Neisseria bacilliformis (27,509), Corynebacterium matruchotii (12,641), Cutibacterium acnes (11,078), E. corrodens (12,967), C. albicans (4452), Trichomonas tenax (723) | 128.64 | BAL culture: K. pneumoniae, C. albicans |
| 28 | Not done | Sputum | tNGS | P. jirovecii (117), HHV-7(11) | < 37.5 | None |
| 29 | Negative | BAL | tNGS | P. jirovecii (4137), P. aeruginosa (27), E. coli (14), T. whipplei (749) | Not done | BAL culture: P. aeruginosa |
| 30 | Negative | BAL | tNGS | P. jirovecii (655), T. whipplei (14) | < 37.5 | None |
| 31 | Negative | BAL | mNGS | P. jirovecii (878), T. whipplei (234), Torque teno virus (510), CMV (200), S. pseudopneumoniae (280), Streptococcus oralis (57), H. parainfluenzae (73), H. haemolyticus (10), G. adiacens (14), R. mucilaginosa (13) | 87.61 | None |
| 32 | Not done | Sputum | tNGS | K. pneumoniae (6055), H. haemolyticus (1738), EBV (330), S. aureus (94), T. whipplei (366), HHV-7 (77), P. jirovecii (32), HHV-6 (11), CMV (5) | Not done | None |
| 33 | Not done | Sputum | tNGS | H. haemolyticus (1960), HHV-7 (365), P. jirovecii (274), T. asahii (1), EBV (34), C. albicans (7) | 87.6 | None |
| Not done | Sputum | tNGS | H. haemolyticus (1385), H. influenzae (14,635), HHV-7 (548), EBV (77), P. jirovecii (45), C. albicans (20) | None | ||
| Not done | BAL | tNGS | P. jirovecii (189), C. albicans (23), CMV (6), HHV-7 (4) | None | ||
| 34 | Not done | Sputum | tNGS | C. albicans (20,746), A. baumannii (1112), K. pneumoniae (340), P. jirovecii (260) | 76.97 | Sputum culture: A. baumannii, C. albicans |
| 35 | Not done | BAL | tNGS | Nontuberculosis mycobacteria (185), P. jirovecii (52) | Not done | None |
| 36 | Negative | Sputum | tNGS | K. pneumoniae (24,020), H. influenzae (8038), EBV (199), C. albicans (163), A. baumannii (41), HHV-7 (36), P. jirovecii (27) | < 37.5 | BAL culture: K. pneumoniae |
| 37 | Negative | BAL | tNGS | P. jirovecii (9600), T. whipplei (8) | 225.8 | None |
| 38 [20] | Positive | BAL | tNGS | P. jirovecii (34,019), CMV (2975), EBV (8), K. pneumoniae (21), C. albicans (2) | 293.99 | Blood and pleural effusion culture: Nocardia kroppenstedtii; BAL culture: K. pneumoniae, N. kroppenstedtii |
| 39 | Negative | BAL | tNGS | Mycobacterium tuberculosis complex (43,834), P. jirovecii (927) | < 37.5 | BAL for AFB smear: positive; BAL for M. tuberculosis DNA: positive |
| 40 | Positive | BAL | tNGS | P. jirovecii (25,284), EBV (17) | < 37.5 | None |
| 41 | Positive | BAL | tNGS | P. jirovecii (58,385), EBV (374), E. faecalis (199) | 93.8 | None |
| 42 | Negative | BAL | tNGS | P. jirovecii (2470) | < 37.5 | None |
| 43 | Negative | BAL | tNGS | HSV-1 (580), E. coli (11), HHV-7 (4), C. albicans (10,441), P. jirovecii (49) | < 37.5 | BAL for HSV DNA: positive |
| 44 | Negative | BAL | tNGS | P. aeruginosa (3638), K. pneumoniae (58), CMV (61), P. jirovecii (47) | < 37.5 | BAL culture: P. aeruginosa |
| 45 | Positive | BAL | tNGS | P. jirovecii (64,629), CMV (81) | < 37.5 | None |
| 46 | Not done | BAL | tNGS | Cryptococcus neoformans (73,023), P. jirovecii (796) | < 37.5 | Serum for cryptococcal antigen: positive |
| 47 | Not done | Sputum | tNGS | P. aeruginosa (6493), H. haemolyticus (80), adenovirus C (12), C. albicans (102), P. jirovecii (62), EBV (23), HHV-7 (4) | < 37.5 | BAL for M. tuberculosis complex tNGS: 11 reads |
| 48 | Not done | BAL | tNGS | K. pneumoniae (56,021), P. aeruginosa (18,635), S. aureus (2661), P. jirovecii (1108), EBV (792) | Not done | BAL culture: K. pneumoniae, P. aeruginosa |
| 49 | Not done | Sputum | tNGS | K. pneumoniae (37,575), S. aureus (13,401), P. aeruginosa (13,123), H. haemolyticus (25), C. albicans (6927), P. jirovecii (201) | < 37.5 | None |
| 50 | Not done | BAL | tNGS | K. pneumoniae (73,975), P. jirovecii (56), CMV (12) | < 37.5 | BAL culture: K. pneumoniae |
| 51 | Not done | Sputum | tNGS | H. haemolyticus (25), T. whipplei (1373), P. jirovecii (202) | Not done | Throat swab for SARS-CoV-2 RNA: positive |
| 52 | Negative | BAL | mNGS | K. pneumoniae (177), P. jirovecii (11), HHV-6B (1), Corynebacterium propinquum (442,826), Dolosigranulum pigrum (140,682), V. parvula (76,864), C. acnes (39,845), Prevotella salivae (32,519), A. dentalis (2687), Megasphaera micronuciformis (6162), Moraxella nonliquefaciens (3916), C. concisus (4279), S. epidermidis (2934), Streptococcus anginosus (855), S. salivarius (588), C. albicans (5555) | < 37.5 | None |
| 53 | Negative | BAL | tNGS | P. jirovecii (27) | < 37.5 | None |
BAL, Bronchoalveolar lavage; NGS, Next-generation sequencing; tNGS, Targeted NGS; mNGS, Metagenomics NGS; EBV, Epstein-Barr virus; CMV, Cytomegalovirus; HHV, Human herpes virus; HSV, Herpes simplex virus; AFB, Anti-fast bacilli; NPS, Nasopharyngeal swab; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2