Distribution Patterns of Pathogens Causing Lower Respiratory Tract Infection Based on Metagenomic Next-Generation Sequencing

Figures & data

Table 1 Characteristics of the Patients

Characteristics	Patients^#, n (%)
Age, years, mean ± standard deviation	60.1 ± 15.0
Gender
Male (%)	86 (62.8%)
Female (%)	51 (37.2%)
Infection types (n=137)
Pneumonia	75 (54.7%)
Severe pneumonia	35 (25.5%)
Tuberculosis	9 (6.6%)
Lung abscess	7 (5.1%)
AECOPD	5 (3.6%)
Bronchitis	1 (0.7%)
Other pulmonary infection	13 (9.5%)
Non-infection	3 (2.2%)
Any comorbidity, n (%)
Bronchiectasis	4 (2.9%)
COPD	1 (0.7%)

Notes: ^#Individual patients may have multiple diagnosis. Other pulmonary infection including interstitial lung disease, pulmonary shadow patients with pathogens detected, and finally diagnosed with pulmonary infection patients. Non-infection represents patients had aberrant lung imaging, negative pathogen findings from mNGS and CMT testing, and a diagnose of unclear infection type.

Abbreviations: AECOPD, acute exacerbation chronic obstructive pulmonary disease; COPD, chronic obstructive pulmonary disease.

Figure 1 Flow diagram of patient’s inclusion in this study.

Figure 2 Pathogen detection rate and concordance between CMT and mNGS. (A) The positive rate of mNGS for different kinds of specimen. (B) The positive rate of CMT and mNGS results. P value present with ****Indicating less than 0.0001. (C) Concordance of detected pathogens between mNGS and CMT.

Table 2 The Samples with Only Positive Pathogen Results by CMT

Sample ID	Diagnosis	mNGS Specimen	CMT Specimen	CMT Results^#
10	Pulmonary infection	Blood	BALF	EBV
12	Pneumonia	BALF	Sputum	Candida albicans
17	Severe pneumonia	Blood	Sputum	Candida albicans
20	Pneumonia	BALF	BALF	Pseudomonas aeruginosa
23	Pneumonia	Tissue	Sputum	Candida albicans
37	Severe pneumonia	BALF	Sputum	Candida albicans
56	Severe pneumonia	Blood	Sputum	Candida albicans
75	Severe pneumonia	Blood	Serum	Fungi
103	Pneumonia	BALF	Serum	Fungi

Note: Fungi means the pathogen was detected by G test.

Abbreviation: ^#EBV, Epstein-Barr virus.

Figure 3 Pathogens identified by CMT and mNGS. (A) Veen diagram showed the overlapped numbers of pathogen species detected by mNGS and CMT. (B) The type of infected pathogens for the patients based on the CMT and mNGS results.

Figure 4 Pathogen profiles detected by mNGS and CMT.

Figure 5 Seasonal prevalence of the pathogens detected by both mNGS and CMT.

Figure 6 Seasonal prevalence of the pathogens detected by mNGS. (A) The distribution of gram-negative bacteria. (B) The distribution of gram-positive bacteria. (C) The seasonal prevalence of fungi. (D) Virus distribution based on seasons. “Other” represents the set of bacteria present in only one sample.

Figure 7 Heatmap of pathogens in samples with at least one consistent pathogen between mNGS and CMT.