Table 3.

The detail information of samples with conflicting results.

Patient ID	Smear results	Culture results	Histopathology results	Potential pathogens by mNGS	Other laboratory-based diagnostic testing results	Clinical diagnosis of pulmonary disorders
P2	Fungal hypha	Negative	Several acid-fast bacteria	MTBC Haemophilus influenzae	MTBC positive by quantitative real-time PCR WBC 14.80 × 10∧9/L (↑)	Pulmonary occupying lesion
P6	Gram-negative bacilli	Negative	Adenocarcinoma	Negative	MTBC negative by GeneXpert CRP 1.5mg/L PCT < 0.02ng/ml	Lung cancer (adenocarcinoma)
P14	Negative	Aspergillus fumigatus	Scattered lymphocyte infiltration; granuloma formation	MTBC	MTBC positive by GeneXpert	Pulmonary tuberculosis (high probability)
P20	Fungal septatehypha	Penicillium	Fungal hypha (probable filamentous fungi except for Aspergillus and Zygomycetes)	Neisseria meningitidis	WBC 11.06 × 10∧9/L (↑) CRP 16.62 mg/L (↑) MTBC negative by quantitative real-time PCR	Pulmonary infection

MTBC, Mycobacterium tuberculosis complex; PCR, polymerase chain reaction; WBC, white blood cell count; CRP, C-reactive protein; PCT, procalcitonin.

Up arrow (↑) indicated that the result was higher than normal reference range.