Table 4.
Results of rapid metagenomics, clinical diagnosis and medical records of patients with typical fastidious pathogens, S. pneumoniae, H. influenzae and M. catarrhalis.
| Age | Sex | Sample type a | Clinical department b | Type of infection c | Comorbidities | Complication d | Empiric therapy |Switched therapy e | PCT f (ng/mL) | CRP g (mg/L) | Outcome | LOS h (Days) c | Rapid metagenomics result | Comments i |
|---|---|---|---|---|---|---|---|---|---|
| (Patients with S. pneumoniae identified by rapid metagenomics and urine antigen test) | |||||||||
| 57 | F | B | RICU | SCAP | None | Sepsis; RF | LVF+CRO+IPM | LVF; PIP/TAZ | 5.48 | 372 | Recovered | 23 | S. pneumoniae (98.7%) | Early de-escalation would be achieved when clinicians knew Meta, as good as urinary antigen. |
| 33 | M | B | RICU | SCAP | None | ARDS; RF | MFX | 8.49 | 44.5 | Recovered | 8 | R. mucilaginosa (21.5%); S. pneumoniae (10.8%) | |
| 44 | M | B | Ward | CAP-ICH | NS; Diabetes; Influenza | None | PIP/TAZ+MFX | AMC | 0.58 | 11 | Recovered | 9 | S. pneumoniae (96.8%) | |
| (Patients with S. pneumoniae identified by rapid metagenomics and culture) | |||||||||
| 70 | M | S | Ward | HAP (late-onset) |
CTEPH; Chronic pulmonary heart disease | Cardiogenic shock | FOX | CSL | 0.26 | 21 | Dead | 15 |
L. rhamnosus (24.5%); S. pneumoniae (12.3%); S. parasanguinis(11.0%); R. dentocariosa(10.6%) |
Narrow spectrum antibiotics could be chosen when S. pneumoniae was the most likely pathogen from Meta of’ sputum. |
| 82 | M | S | Ward | CAP | Tuberculous pleurisy; GERD | None | LVF | 0.28 | 19 | Recovered | 11 |
S. parasanguinis (18.8%); S. salivarius (18.3%); R. mucilaginosa(15.4%); S. pneumoniae (6.7%) |
|
| 78 | M | S | Ward | AECOPD II | None | None | / | 5 | Recovered | 3 |
C. argentoratense (24.2%); S. mitis (20.0%); S. pneumoniae (12.3%) |
|
| (Patients with S. pneumoniae identified by rapid metagenomics and qPCR) | |||||||||
| 84 | M | B | RICU | SCAP | COPD; Chronic pulmonary heart disease; GERD | Sepsis; RF | CSL+AZM | CSL; LVF; VCM | 5.36 | 39.1 | Dead | 30 | S. pneumoniae (58.3%) | De-escalation was not achieved because the clinicians did not know the causative pathogens. |
| 75 | M | S | Ward | HAP (early-onset) |
Cerebral infarction; Mental disorders | None | ETP | 0.17 | 59 | Recovered | 10 | S. pneumoniae (64.3%) | |
| 77 | F | S | Ward | AEBX | None | CSL | 0.55 | 177 | Recovered | 14 |
S. mitis (55.5%); S. pneumoniae (10.5%); P. aeruginosa (1.3%) |
|
| 56 | M | B | RICU | SCAP | Influenza | RF; ARDS | PIP/TAZ+LVF | 9.89 | 38.07 | Recovered | 19 | S. pneumoniae (78.7%); C. striatum (6.7%) | |
| 71 | M | B | Ward | Lung abscess | Metastatic carcinoma of lung; Colorectal cancer | None | CSL | PIP/TAZ | 0.13 | 70 | Recovered | 23 | S. pneumoniae (80.0%) | |
| 65 | M | S | Ward | AECOPD II | Lung cancer; GERD | None | None | / | 24 | Recovered | 29 |
R. mucilaginosa (16.9%); S. pseudopneumoniae (12.1%); S. pneumoniae (6%) |
|
| 52 | F | S | Ward | AEBX | GERD | None | PIP/TAZ | 0.29 | 6 | Recovered | 7 |
P. aeruginosa (53.5%); S. mitis (19.0%); S. parasanguinis (6.4%); S. pneumoniae (5.2%) |
|
| (Patients with S. pneumoniae identified by rapid metagenomics only) | |||||||||
| 59 | M | B | Ward | Lung abscess | Diabetes | None | PIP/TAZ+ORN | 0.29 | 58 | Recovered | 49 |
P. aeruginosa (24.3%); S. mitis (26.2%); P. micra(15.9%); S. pneumoniae (5.6%) |
Non-verification might be low-abundance of S. pneumoniae. |
| 88 | M | S | Ward | CAP-ICH | NHL; Chemotherapy; GERD; Lacunar infarction | Sepsis | MOX | MOX; LVF; MEPM; VCM | 1.15 | 47 | Recovered | 32 | S. mitis (56.1%); S. pneumoniae (11.3%) | |
| 69 | F | S | Ward | CAP-ICH | Multiple Myeloma; GERD | Cardiac failure; Pleural effusion | MOX | PIP/TAZ; LVF; AMK; TGC | 0.69 | 23.5 | Recovered | 21 |
R. mucilaginosa (27.2%); L. pentosus (14.2%); V. parvula(14.0%); E. faecium (3.1%); S. pneumoniae (1.7%) |
|
| (Patients with H. influenzae identified by rapid metagenomics and culture) | |||||||||
| 70 | F | B | Ward | CAP | Bronchiectasis | None | CRO | / | 12 | Recovered | 12 | H. influenzae (93.2%) | Narrower spectrum antibiotics should be used. |
| 74 | F | B | Ward | HAP (early-onset) |
Sjögren’s syndrome; ILD | None | INH | INH; MFX | 0.4 | 85 | Recovered | 19 | H. influenzae (88.4%); M. intracellulare (8.1%) | |
| 65 | F | B | Ward | AEBX | None | None | 0.26 | 6 | Recovered | 6 | H. influenzae (89.1%) | |
| (Patients with H. influenzae identified by rapid metagenomics and qPCR) | |||||||||
| 60 | F | B | Ward | AEBX | None | CAZ | 0.02 | 2 | Recovered | 7 | H. influenzae (98.1%) | Early de-escalation would be achieved if the clinicians knew Meta. |
| 60 | M | B | RICU | AECOPD II | Chronic pulmonary heart disease | RF | PIP/TAZ+LVF | 0.09 | 1.66 | Recovered | 12 | H. influenzae (80.6%) | |
| 68 | M | S | Ward | AEBX | Diabetes | None | CAZ | 0.26 | 7 | Recovered | 8 | H. influenzae (20.8%) | |
| 81 | F | S | Ward | CAP | Chronic bronchitis; PAH; Chronic cardiac insufficiency | Pleural effusion | MFX | CAZ | 0.21 | 3 | Recovered | 16 | H. influenzae (29.4%); L. rhamnosus (15.1%) | |
| 38 | M | S | Ward | AEBX | Lung transplant; Emphysema | RF | PIP/TAZ | 1.77 | 59 | Recovered | 7 |
C. striatum (48.9%); H. influenzae (20.1%); S. anginosus(15.6%) |
|
| 43 | F | S | SICU | HAP (late-onset) |
None | Brainstem hemorrhage | CRO | PIP/TAZ; CAZ | 2.55 | 92.62 | Recovered | 27 | H. influenzae (64.4%); P. aeruginosa (16.4%) | H. influenzae and P. aeruginosa co-infection confirmed by both clinical diagnosis and Meta. |
| 90 | M | S | Ward | AECOPD I | TB | None | CAZ | ETP; PIP/TAZ | 13.8 | 53 | Recovered | 13 | H. influenzae (37.5%); P. aeruginosa (12.5%) | |
| 60 | F | S | Ward | AEBX | AECOPD; PAH; Diabetes; Sjögren’s syndrome | None | None | 0.3 | 5 | Recovered | 11 |
H. influenzae (56.0%); P. aeruginosa (32.7%); R. mucilaginosa (5.7%) |
|
| 65 | M | B | Ward | CAP-ICH | Esophageal cancer; Chemotherapy | Myelosuppression | PIP/TAZ+TMP | 0.23 | 5.41 | Recovered | 9 |
P. aeruginosa (85.7%); H. influenzae (4.5%); S. anginosus (2.8%) |
|
| (Patients with M. catarrhalis identified by rapid metagenomics and culture) | |||||||||
| 56 | M | B | RICU | AEBX | Chronic pulmonary heart disease | RF | CIP+CAZ | CIP; CAZ; AZM | 0.55 | 109.56 | Recovered | 19 | M. catarrhalis (97.4%) | M. catarrhalis in AEBX and AECOPD rapidly identified by Meta. |
| 72 | M | S | Ward | AECOPD II | Chronic bronchitis | None | None | / | 13 | Recovered | 4 | M. catarrhalis (92.4%); R. mucilaginosa (1.7%) | |
| 54 | F | S | Ward | AECOPD II | None | None | / | 7 | Recovered | 17 | S. parasanguinis (20.3%); M. catarrhalis(18.4%); V. atypica (13.0%) | |
| 67 | M | S | Ward | AECOPD II | Chronic pulmonary heart disease | None | None | / | 8 | Recovered | 6 | P. aeruginosa (69.1%); M. catarrhalis (27.3%) | |
| (Patients with M. catarrhalis identified by rapid metagenomics and qPCR) | |||||||||
| 54 | M | B | RICU | SCAP | GRED | RF; Sepsis; Pleural effusion | PIP/TAZ | IPM; VCM | 0.02 | 2 | Dead | 5 | M. catarrhalis (18.4%) | De-escalation was not achieved because the clinicians did not know the causative pathogens. |
| 87 | M | S | Ward | AECOPD II | GRED; Cardiac insufficiency | None | ZOX | 0.29 | 22 | Recovered | 14 | M. catarrhalis (87.9%); R. mucilaginosa (9.4%) | |
| 62 | M | B | RICU | CAP-ICH | Rheumatoid arthritis; Rheumatoid lung disease; Diabetes; GRED; Cardiac insufficiency | None | ZOX+LVF | 0.05 | 96.19 | Recovered | 6 |
M. catarrhalis (24.0%); V. atypica (10.2%); R. mucilaginosa (8.4%) |
|
| 72 | M | S | Ward | AECOPD I | Bronchiectasis | RF | CSL+LVF | 53 | 53 | Recovered | 5 | M. catarrhalis (88.8%); R. mucilaginosa (1.2%) | |
| 58 | M | B | Ward | AECOPD II | Pulmonary interstitial fibrosis; Diabetes | None | MFX+CSL | 0.21 | 3.41 | Recovered | 13 | M. catarrhalis (12.5%) | |
a
Gender: M, Male; F, Female. Sample type: S, Sputum; B, Bronchoalveolar lavage fluid.
b
RICU, Respiratory intensive care unit; SICU, Surgical intensive care unit
c
CAP, community acquired pneumonia; SCAP, severe community acquired pneumonia; HAP, hospital acquired pneumonia; AECOPD, acute exacerbation of chronic obstructive pulmonary disease, AnthonisenⅠ/Ⅱ; AEBX, Acute exacerbation of bronchiectasis
d
CTEPH, chronic thromboembolic pulmonary hypertension; NS, Nephrotic syndrome; GERD, Gastroesophageal reflux disease; PAH, pulmonary arterial hypertension; TB, Tuberculosis; ILD, Interstitial lung disease; RF, Respiratory failure; NHL, non-Hodgkin’s lymphoma.
e
If the antibiotics are not changed, only empirical therapy was reported.
AMC, Amoxicillin/clavulanic acid; AZM, Azithromycin; AMK, Amikacin; CAZ, Ceftazidime; CSL,Cefperazone/Sulbactam; CRO, Ceftriaxone; CIP, Ciprofloxacin; ETP, Ertapenem; FOX, Cefoxitin;
INH,Isoniazide; IPM, Imipenem; LVF, Levofloxacin; MFX, Moxifloxacin; MOX, Latamoxef; MEPM, Meropenem; ORN, Ornidazole; PIP/TAZ, Piperacillin/tazobactam; TGC, Tigecycline; TMP, Trimethoprim; VCM, Vancomycin; ZOX, Ceftizoxime.
f
PCT, Procalcitonin.
g
CRP, C-reactive protein.
h
Length of stay.
i
Meta, rapid metagenomics or identification results of rapid metagenomic.