Comparison between cultivation and sequencing based approaches for microbiota analysis in swabs and biopsies of chronic wounds

Abstract

Chronic wounds are a prominent health concern affecting 0.2% of individuals in the Western population. Microbial colonization and the consequent infection contribute significantly to the healing process of chronic wounds. We have compared cultivation and 16S amplicon sequencing (16S-AS) for the characterization of bacterial populations in swabs and biopsy tissues obtained from 45 chronic wounds and analysed metadata for wound-specific and clinical-outcome-associated correlations with bacterial community structure. Using cultivation approach, we detected a total of 39 bacterial species, on average 2.89 per sample (SD=1.93). Comparison of cultivation results between swabs and biopsy samples showed no significant advantage of one sampling method over the other. 16S-AS was advantageous in comparison to the cultivation approach in case of highly diverse communities, where we could additionally detect numerous obligate and facultative anaerobic bacteria from genera Anaerococcus, Finegoldia, Porphyromonas, Morganella and Providencia. Based on the community diversity, chronic wound microbiota could be distributed into three groups, however, no correlation between groups and clinical outcome was observed. Clinically estimated presence of biofilm and a larger surface area at the initial visit were most significantly associated with unfavourable clinical outcomes after one-year follow-up visit. Corynebacterium was the single most predictive bacterial genus associated with unfavourable clinical outcomes in our study.