Early Identification of Fungal and Mycobacterium Infections in Pulmonary Granulomas Using Metagenomic Next-Generation Sequencing on Formalin fixation and paraffin embedding tissue

ABSTRACT

Background

The purpose of the study is to assess the etiology detection ability of Metagenomic Next-Generation Sequencing (mNGS) on formalin fixation and paraffin embedding (FFPE) tissue from postoperative biopsy specimens.

Methods

We prospectively enrolled specimens from patients undergone surgery biopsy due to undefinite diagnosis and pathologically indicated granulomatous lesions. FFPE tissues were tested by mNGS and histopathology. The etiology detection rate of mNGS was calculated and compared with histopathology..

Results

Among the 69 cases eventually included, 41 (59.42%) were diagnosed with infectious granuloma. The overall fungi and mycobacteria etiology detection rates of mNGS in granuloma lesions was 87.80% (36/41). The mNGS increased the detection rate by 68.29% (28/41) compared with histopathology, the difference was statistically significant (χ2 = 28.97, P = 0.00). The detection rates of mNGS in fungal infections (12/12,100%) and in mycobacterium infections (22/27, 81.48%) were significant higher than those of histopathology (8/12, 66.67% and 0/27, 0.00%; both P = 0.00). Two (2/2.100%) cases of co-infection were detected at one time by mNGS. All mNGS-based clinical decisions were made within 2 days.

Conclusions

The mNGS could accurately and quickly detect fungi and mycobacteria in FFPE specimens from postoperative granuloma specimens and identify the pathogens to the species level.

Clinical Trials Registration

China Clinical Trial Registry ChiCTR2000035464

KEYWORDS:

• Metagenomic next-generation sequencing
• formalin-fixed paraffin-embedded
• histopathologic
• fungal granuloma
• mycobacterium granuloma
• etiological diagnosis

Acknowledgments

The authors thank all participants in this study for their time and efforts.

Author contributions statement

Wenwen Sun, Yiming Zhou, Hongcheng Liu: research design, case collection, manuscript writing; ZhengWei Dong, Kunlong Xiong: case collection, data statistics; Lin Fan, Zhemin Zhang: research design, case collection, and manuscript revision.

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer disclosures

Papers of special note have been highlighted as: * of interest, ** of considerable interest.

Additional information

Funding

Funding The study was supported by the fund of Shanghai committee of science and technology (No:21Y119010000) and the fund of Shanghai pulmonary hospital (No:FK1945).