Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections.

We conducted a single-center retrospective study to investigate impact of mNGS on focal infection diagnosis and compared it with conventional methods, including culture, pathological examination, Xpert MTB/RIF, etc. 98 suspected focal infections cases were enrolled, and medical records were reviewed to determine their rates of detection, time-to-identification, and clinical outcomes.

mNGS showed a satisfying diagnostic positive percent agreement of 86.30% (95% CI: 75.79–92.88%) in a variety of tissues, compared to 45.21% (95% CI: 33.68–57.24%) for culture and 57.53% (95% CI: 45.43–68.84%)f for conventional methods (p < 0.0125), and detected an extra 34 pathogenic microorganisms. Time requirement for pathogen identification using mNGS ranges from 31 h to 55 h, which showed an advantage over culture. (82.36 h; 95%CI: 65.83, 98.89; P < 0.05)

mNGS showed promising potential in pathogenic diagnosis during focal infections and might enable clinicians to make more timely and targeted therapeutic decisions.