Table 1.

Characteristics of pulmonary critically ill patients with COVID-19 and positive for fungi by metagenomic analysis.

Characteristics	Patient #1	Patient #2	Patient #3	Patient #4	Patient #5	Patient #6	Patient #7	Patient #8	Patient #9	Patient #10
Demographics and clinical characteristics
Gender	M	M	F	M	M	F	M	M	M	M
Age (years)	41	55	62	54	53	44	32	76	73	83
Diagnosis for COVID-19	PCR, mNGS	Antigen	PCR	PCR	Antigen	PCR, mNGS	PCR	PCR, mNGS	PCR	PCR, mNGS
Medical history	Hypertension, type 2 diabetes, kidney transplant status	Acute kidney injury, liver transplant status	Hypertension, nephritic syndrome	Hypertension, type 2 diabetes, liver abscess after percutaneous drainage	Thymoma B3	Hypertension, kidney transplant status	No	Coronary atherosclerotic heart disease after PCI, liver cirrhosis, hypersplenism, old cerebral infarction, type 2 diabetes, hypertension	No	Hypertension, coronary heart disease
Current smoker	Yes	No	No	Yes	No	No	Yes	No	No	No
Underlying immunocompromising condition	Steroids, tacrolimus, mycophenolate	Tacrolimus, mycophenolate, sirolimus	Mycophenolate	No	Oxaliplatin + cyclophosphamide + doxorubicine chemotherapy	Steroids, tacrolimus, mycophenolate	No	No	No	No
Cause of admission to the ICU	ARDS	ARDS	ARDS	ARDS, cerebral infarction, cerebral hernia, septic shock	ARDS	ARDS	ARDS, acute pancreatitis	ARDS	ARDS	ARDS, cardiopulmonary arrest after cardiopulmonary resuscitation
Time from illness onset to ICU admission, days	14	24	10	4	3	42	1	11	30	20
ARDS	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
PaO2 (ICU admission)	71	92	43	94	69	70	99	64	48	75
FIO2 (ICU admission)	0.90	0.95	0.61	0.41	0.7	0.60	0.41	0.81	1.00	0.80
Horowitz Index (ICU admission)	79	97	70	229	99	117	241	79	48	94
Prone positioning	Yes	Yes	Yes	No	No	No	Yes	Yes	No	No
Tracheal intubation	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
SOFA score (ICU admission)	7	8	4	7	6	7	4	7	9	8
CURB-65 score (ICU admission)	2	2	2	2	1	2	1	2	3	3
APACHE II score (ICU admission)	12	34	18	22	19	12	11	14	24	35
CAPA classification	Probable	Possible	Probable	Probable	Possible	Probable	Probable	Probable	Possible	Possible
Laboratory findings
mNGS (first time after ICU admission)
Specimen	BALF & PB	BALF & PB	BALF	BALF	BALF	BALF	BALF	BALF	BALF	BALF
Fungus	Aspergillus fumigatus (PB & BALF) Aspergillus niger (BALF) Pneumocystis jeroveci (BALF)	Aspergillus flavus/Aspergillus oryzae(BALF) Aspergillus fumigatus (PB)	Aspergillus fumigatus Aspergillus flavus	Aspergillus fumigatus	Aspergillus fumigatus	Aspergillus flavus Aspergillus fumigatus	Aspergillus flavus/Aspergillus oryzae Rhizopus oryzae	Aspergillus flavus/Aspergillus oryzae Aspergillus fumigatus	Aspergillus flavus Aspergillus terreus Clavispora lusitaniae	Aspergillus fumigatus Candida albicans
Bacteria	Enterococcus faecium (BALF) Leuconostoc lactis (BALF) Tropheryma whipplei (BALF)	Klebsiella pneumoniae (BALF & PB) Acinetobacter baumannii (BALF)	No	Klebsiella pneumoniae Streptococcus pneumoniae Acinetobacter baumannii Enterococcus faecium	Acinetobacter baumannii	Enterococcus faecium Acinetobacter pittii	Escherichia coli Klebsiella pneumoniae	Acinetobacter baumannii	Klebsiella pneumoniae Enterococcus faecium	No
Virology1	Epstein–Barr virus (PB) Human betaherpesvirus 5 (BALF) SARS-CoV-2 (BALF)	Human alphaherpesvirus 1 (PB) Epstein–Barr virus (PB)	No	Human alphaherpesvirus 1 Epstein–Barr virus	Human betaherpesvirus 5	Torque teno virus SARS-CoV-2	No	SARS-CoV-2	No	SARS-CoV-2
Serum galactomannan (µg/L) [<0.85]2	0.43	0.47	0.31	0.12	0.81	0.84	1.94	0.96	NA	0.28
Serum β-D-glucan (pg/mL) [0-95]	<10	<10	<10	171.11	<10	294.35	126.97	<10	NA	<10
BALF galactomannan (pg/mL) [<1]	0.48	0.36	NA	NA	NA	0.36	3.87	1.26	NA	NA
Sputum culture	Negative	Acinetobacter baumannii	NA	Acinetobacter baumannii	Negative	Negative	Acinetobacter baumannii	Acinetobacter baumannii	NA	NA
BALF culture	Aspergillus flavus	Acinetobacter baumannii	Aspergillus fumigatus Aspergillus flavus	Negative	Negative	Negative	Escherichia coli Aspergillus flavus	Acinetobacter baumannii	Klebsiella pneumoniae	Negative
Pheripheral blood culture	Negative	Enterococcus faecium Klebsiella pneumoniae	Negative	Negative	Negative	Negative	Negative	Negative	Enterococcus faecium	Candida albicans
Treatment
Steroids to treat pneumonia	Yes	Yes	No	Yes	Yes	Yes	No	Yes	Yes	No
Antifungal	Voriconazole, Amphotericin B, Sulfamethoxazole	Voriconazole, Amphotericin B	Voriconazole	Voriconazole	Voriconazole	Voriconazole	Isavuconazole Amphotericin B	Voriconazole	No	No
Antiviral (besides COVID-19)	Penciclovir	Ganciclovir	No	No	No	Ganciclovir	No	No	No	No
Anti-COVID-19	Azvudine, Paxlovid	Paxlovid	Azvudine, Paxlovid	No	No	Paxlovid	No	Azvudine, Paxlovid	Azvudine, Paxlovid	No
Antibacterial	Meropenem, Linezolid	Ceftazidime and Avibactam Sodium, Polymyxin B	Ceftizoxime	Meropenem, Ceftazidime, and Avibactam Sodium	Imipenem and cilastatin sodium, Teicoplanin	Biapenem, Linezolid	Imipenem and Cilastatin Sodium, Ceftazidime and Avibactam Sodium, Teicoplanin	Moxalactam Cefoperazone Sodium and Sulbactam Sodium	Cefoperazone Sodium and Sulbactam Sodium	Imipenem and Cilastatin Sodium
Outcomes
Acute renal failure	Yes	Yes	No	No	Yes	No	No	No	No	Yes
Renal replacement therapy	Yes	Yes	No	No	Yes	No	No	No	No	Yes
Vasopressor	Yes	Yes	No	Yes	Yes	No	Yes	No	No	Yes
ECMO	No	No	No	No	Yes(V-A)	No	Yes (V-V)	No	No	Yes (V-V)
Outcome	Died	Survived	Survived	Died	Died	Survived	Survived	Died	Died	Died

APACHE, Acute Physiology and Chronic Health Evaluation; ARDS, acute respiratory distress syndrome; BALF, bronchoalveolar lavage fluid; CAPA, COVID-19-associated pulmonary aspergillosis; CURB-65, Confusion, Urea, Respiratory rate, Blood pressure plus age ≥ 65 years; ECMO, extracorporeal membrane oxygenation; FIO₂, fraction of inspiration oxygen; ICU, intensive care unit; mNGS, metagenomic next-generation sequencing; NA, not available; PaO₂, partial pressure of oxygen; PB, peripheral blood; PCI, percutaneous coronary intervention; PCR, polymerase chain reaction; SOFA, Sequential Organ Failure Assessment; V-A, venoarterial; V-V, venovenous.

¹In patient #2, #3, #4, #5, #7, and #9, only DNA sequencing was performed and no SARS-CoV-2 was detected.

²Normal reference range of our laboratory was given in square brackets. The same below.