Table 3. The detailed information of samples with conflicting results.

Patient ID	Specimen	NGS result (specific reads)	Culture results	Other microbiological diagnostic testing results	Clinical diagnosis	Underlying diseases
5	Plasma	Negative	Corynebacterium	ND	Bloodstream infection	Severe polymorphic erythema
10	Plasma	Negative	Clostridium capsulatum	ND	Bloodstream infection	Nephrotic syndrome
27	BAL	Streptococcus gordonii [558]	Aspergillus fumigatus	GM test (+), G test (+), BAL smear (−)	Pulmonary infection	Rheumatoid arthritis
31	Puncture Liquid	Clostridium necrosis [117]	Mucor, Clostridium necrosis	G test (+)	Liver abscess	Systemic lupus erythematosus
95	BAL	Moraxella spp [344], EBV [3,293]	Candida albicans	EBV-DNA (+), G test (+), BAL smear: Candida albicans (+)	Pulmonary infection	Systemic lupus erythematosus
101	Plasma	Staphylococcus aureus [1,316]	Escherichia coli	ND	Bloodstream infection	Pemphigus
106	Plasma	Enterococcus faecium [74]	Cryptococcus neoformans	Latex agglutination test (+,1:320), G test (−)	Disseminated cryptococcosis	Primary biliary cirrhosis
17	Biopsy Tissue	Staphylococcus aureus [118]	Negative	ND	No infection (primary disease)	Subacute thyroiditis, autoimmune liver disease
21	Plasma	Acinetobacter baumannii [689]	Negative	ND	No infection (drug fever)	Rheumatoid arthritis
27	BAL	Candida albicans [374]	Negative	Filmarray respiratory panel test (−), G test (−)	No infection (primary disease)	ANCA-associated vasculitis
87	Plasma	Pseudomonas aeruginosa [885]	Negative	ND	No infection (drug fever)	Systemic lupus erythematosus

G test, (1,3)-β-D-glucan test. EBV, Epstein-Barr virus; BAL, bronchoalveolar lavage; GM test, Galactomannan test; ND, no data.