The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform

Abstract

Introduction: Metagenomic next-generation sequencing (mNGS) has been increasingly used to detect infectious organisms and is rapidly moving from research to clinical laboratories. Presently, mNGS platforms mainly include those from Illumina and the Beijing Genomics Institute (BGI). Previous studies have reported that various sequencing platforms have similar sensitivity in detecting the reference panel that mimics clinical specimens. However, whether the Illumina and BGI platforms provide the same diagnostic performance using authentic clinical samples remains unclear. Methods: In this prospective study, we compared the performance of the Illumina and BGI platforms in detecting pulmonary pathogens. Forty-six patients with suspected pulmonary infection were enrolled in the final analysis. All patients received bronchoscopy, and the specimens collected were sent for mNGS on the two different sequencing platforms. Results: The diagnostic sensitivity of the Illumina and BGI platforms was notably higher than that of conventional examination (76.9% vs. 38.5%, p < 0.001; 82.1% vs. 38.5%, p < 0.001; respectively). The sensitivity and specificity for pulmonary infection diagnosis were not significantly different between the Illumina and BGI platforms. Furthermore, the pathogenic detection rate of the two platforms were not significantly different. Conclusion: The Illumina and BGI platforms exhibited similar diagnostic performance for pulmonary infectious diseases using clinical specimens, and both are superior to conventional examinations.

Keywords: BGI; Illumina; conventional examination; metagenomic next-generation sequencing; pulmonary infection.

FIGURE 1

Flow chart depicting the enrollment of patients in this study. CE, conventional examination; BGI, Beijing Genomics Institute.

FIGURE 2

Pathogen distribution (A) in pulmonary infectious disease and (B) initial empiric antibiotic treatment.

FIGURE 3

Comparison of pathogens detected using mNGS (Illumina and BGI platforms) and CE. Among the 39 patients with identified pathogens, 15 (38.46%) were diagnosed using CE (pink circle) and 3 (7.69%) using CE only; 36 (92.31%) were diagnosed using mNGS, 32 (82.05%) using the BGI platform (blue circle), 31 (79.49%) using the Illumina platform (orange circle), 12 (30.77%) using mNGS and CE (the overlap of pink, orange, blue circle). The 27 patients (69.23%) were diagnosed using the Illumina and BGI platforms (overlap between orange and blue circle Illumina and BGI platforms), 4 (10.25%) using only the Illumina platform, and 5 (12.82%) using only the BGI platform.

FIGURE 4

Comparison between the pathogenic detection rates of CE and the mNGS platforms (Illumina and BGI). ***p < 0.001, compared with CE. The x-axis represents the number of cases, while the y-axis represents the detection methods. CE, conventional examinations.

FIGURE 5

Comparison of the Illumina and BGI platforms in detecting different pathogens. No significant difference was observed between the two platforms (p > 0.05). The number of positive samples (x-axis) for pairwise Illumina and BGI platforms is plotted against the bacteria, fungi, virus and mixed infection groups (y-axis).