Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.

Background: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.

Methods: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.

Results: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.

Conclusion: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.

Trial Registration: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).