Pathogen identification by shotgun metagenomics of patients with necrotising soft-tissue infections.

BACKGROUND: Necrotising soft-tissue infections (NSTIs) are life-threatening, requiring broad-spectrum antibiotics. Their etiological diagnosis can be limited by poor performance of cultures and administration of antibiotics before surgery.

OBJECTIVES: We aimed to: (i) compare 16S-targeted metagenomics (TM) and unbiased semi-quantitative pan-microorganism DNA- and RNA-based shotgun metagenomics (SM) with cultures, (ii) identify patients who best benefit from metagenomics approaches, and (iii) detect the microbial pathogens in surrounding non-necrotic "healthy" tissues by SM metagenomics-based methods.

METHODS: A prospective observational study was performed to assess the analytic performance of standard cultures, TM, and SM on tissues from 34 patients with NSTIs. Pathogen identification obtained with these three methods were compared.

RESULTS: Thirty-four necrotic and 10 healthy tissues were collected from 34 patients. The performance of TM was inferior to that of the other methods (p<0.05), whereas SM performed better than standard culture, although the result was not statistically significant (p=0.08). SM was significantly more sensitive than TM for the detection of all bacteria (p=0.02) and standard culture for the detection of anaerobic bacteria (p<0.01). There was a strong correlation (r=0.71, Spearman correlation coefficient) between the semi-quantitative abundance of bacteria in the culture and the bacteria/human sequence ratio in SM. Low amounts of bacterial DNA were found in healthy tissues, suggesting a bacterial continuum between macroscopically "healthy" and necrotic tissue.

CONCLUSIONS: SM showed a significantly better ability to detect a broader range of pathogens than TM and identify strict anaerobes than standard culture. Diabetic patients with NSTIs appeared to benefit most from shotgun metagenomics. Finally, our results suggest a bacterial continuum between macroscopically "healthy" non-necrotic areas and necrotic tissues.