A Comparative Application of Next-Generation Sequencing and Culture-Based Technologies to the Burn Wound Microbiome

Deepak Ozhathil; Caroline Corley; Steven Kahn; Lisa Steed; Henry Ross; Mindy Engevik; Michael Schmidt; Arman Kilic; Carter Powell

Multiple studies have linked bacterial colonization with graft loss and delayed wound healing in burn care. In addition, wound infections are the primary cause of sepsis and death. Unfortunately, culture-based methods have afforded little insight into the microbial makeup of burn wounds. Next Generation Sequencing (NGS) technology represents a promising alternative to traditional wound cultures (TWC), and though validated in other areas of medicine, it has not yet been applied to burn care. 

We hypothesize the premise that NGS is not inferior to TWC at characterizing the microbiota of burn wounds.

The study enrolled adults admitted for surgery of acute burn wounds. A surface wound swab of biofilm and two adjacent tissue specimens were collected from 40 wounds across 25 patients. The swab and one tissue specimen underwent 16S and 18S amplicon sequencing, while the other specimen was sent for TWC (bacterial and fungal speciation). Outcomes were compared using Chi-square and t-tests.

Enrollment favored males (3:1) with a mean age of 47.2 years. Samples were collected 12.3 days post-injury with a mean surface area of injury of 17.7%. TWC identified one species per sample while NGS identified 3.3 on average. Of the 40 samples collected, NGS detected the same or more species in 25, while 15 samples exhibited discrepant results. Eleven of those samples detected species on NGS not identified on TWC. The remaining 4 samples TWC identified microbes that were not detected by NGS – correlating to a non-inferiority of 90% in NGS. NGS identified pathogenic bacterial species in 18 samples and only in 10 samples by TWC. Days till NGS results for bacteria was 2.88 days compared to 4.84 days for TWC. In contrast, fungal cultures resulted 22.62 days later than NGS. Lastly, billable cost per sample was also reduced by a factor of 91.2% for NGS relative to TWC ($250 vs $2,839).

Our preliminary data support the non-inferiority of NGS relative to TWC. NGS offers more robust and earlier detection of microbial species at a reduced cost per sample. Specimens collected closer to the date of injury were predominantly commensal/environmental species, while later specimens revealed enteric/pathogenic incursions. Overall pathogen detection occurred at similar rate between NGS and TWC. In addition, a large number of non-pathogenic species were only detected on NGS, and although some are considered emerging pathogens, their detection is of unclear significance. In conclusion, this study supports the use of NGS as a rapid, accurate and cost effective alternative to TWC with burn wounds.