Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice

TLDR

Metagenomic next‑generation sequencing (mNGS) offers a comprehensive alternative to conventional microbiology, yet its clinical utility remains under‑explored. In a retrospective analysis of 511 clinical specimens collected between April and December 2017, the authors compared mNGS to culture across infectious, noninfectious, and unknown cases and evaluated the impact of prior antibiotic exposure on detection rates. mNGS achieved 50.7 % sensitivity and 85.7 % specificity, outperforming culture—particularly for Mycobacterium tuberculosis, viruses, anaerobes, and fungi—while 61 % of inconclusive culture cases were re‑diagnosed, 58 % lacked empirical antibiotic coverage, and its sensitivity remained higher in antibiotic‑exposed samples, underscoring its promise as a less antibiotic‑affected diagnostic tool.

Abstract

Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited. From April 2017 to December 2017, 511 specimens were collected, and their retrospective diagnoses were classified into infectious disease (347 [67.9%]), noninfectious disease (119 [23.3%]), and unknown cases (45 [8.8%]). The diagnostic performance of pathogens was compared between mNGS and culture. The effect of antibiotic exposure on detection rate was also assessed. The sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7% and 85.7%, respectively, and these values outperformed those of culture, especially for Mycobacterium tuberculosis (odds ratio [OR], 4 [95% confidence interval {CI}, 1.7–10.8]; P < .01), viruses (mNGS only; P < .01), anaerobes (OR, ∞ [95% CI, 1.71–∞]; P < .01) and fungi (OR, 4.0 [95% CI, 1.6–10.3]; P < .01). Importantly, for mNGS-positive cases where the conventional method was inconclusive, 43 (61%) cases led to diagnosis modification, and 41 (58%) cases were not covered by empirical antibiotics. For cases where viruses were identified, broad-spectrum antibiotics were commonly administered (14/27), and 10 of 27 of these cases were suspected to be inappropriate. Interestingly, the sensitivity of mNGS was superior to that of culture (52.5% vs 34.2%; P < .01) in cases with, but not without, antibiotic exposure. mNGS could yield a higher sensitivity for pathogen identification and is less affected by prior antibiotic exposure, thereby emerging as a promising technology for detecting infectious diseases.