The clinical value of metagenomic next generation sequencing in the microbiological diagnosis of skin and soft tissue infections

Published Date
International Journal of Infectious Diseases
Int J Infect Dis. 2020 Sep 5; S1201-9712(20)30721-9
10.1016/j.ijid 2020.09.07
Wang Q
Miao Q
Pan J
Jin W
Ma Y
Zhang Y
Yao Y
Su Y
Huang Y
Li B
Wang M
Li N
Cai S
Luo Y
Zhou C
Wu H
Hu B

Background: Metagenomic next generation sequencing (mNGS) with its comprehensiveness, has been widely applied in microbiological diagnosis. Etiological diagnosis is of paramount clinical importance in patients with skin and soft tissue infections (SSTIs). However, the clinical application of mNGS in SSTIs is relatively less studied.

Materials/methods: From April 1st 2017 to December 31st 2019, 96SSTIs cases were collected. The positive rates of pathogens detected by mNGS and culture were compared by analysing the tissues, pus, swabs and/or interstitial fluids of infected parts. Modification of antibiotic treatment strategy due to mNGS was also assessed.

Results: The sensitivity of mNGS for detecting pathogens in SSTI cases was superior to that of culture testing (67.7% vs 35.4%; p < 0.01). Significantly higher identification rates for viruses (10.4% vs 0.0%; p < 0.01) and anaerobes (11.5% vs 1.0%; p < 0.01) were obtained with mNGS compared to culturing. Notably, rare pathogens such as Vibrio vulnificus and Bartonella henselae were also detected by mNGS. Importantly, proportion of multi-pathogen infections of SSTIs in mNGS was superior to that of culture (16.7% vs 6.3%; p = 0.035). The rate of targeted antibiotic treatment was significantly higher in mNGS-positive cases than that in mNGS-negative cases (41.7% vs 3.8%; p < 0.01). In culture-negative and mNGS-positive cases, the improvement rate was higher than that in mNGS-negative cases but was not statistically significant (75.0% vs 73.1%; p = 0.864).

Conclusions: mNGS is a promising tool for etiological diagnosis of SSTIs, particularly in identifying viruses, anaerobes, and multi-pathogen infections. Application of mNGS testing to clinical practice can change antibiotic treatment strategies and partly benefit clinical outcomes.

Keywords: antibiotic treatment; diagnostic; metagenomic next generation sequencing; sensitivity; skin and soft tissue infections.