| Literature DB >> 34150786 |
Aleksander Mahnic1, Vesna Breznik2, Maja Bombek Ihan3, Maja Rupnik1,4.
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. We have compared two methods, cultivation and 16S amplicon sequencing (16S-AS), for the characterization of bacterial populations in both swabs and biopsy tissues obtained from 45 chronic wounds. Using cultivation approach, we detected a total of 39 bacterial species, on average 2.89 per sample (SD = 1.93), compared to 5.9 (SD = 7.1) operational taxonomic units per sample obtained with 16S-AS. The concordance in detected bacteria between swab and biopsy specimens obtained from the same CWs was greater when using cultivation (58.4%) as compared to 16S-AS (25%). In the entire group of 45 biopsy samples concordance in detected bacterial genera between 16S-AS and cultivation-based approach was 36.4% and in swab samples 28.7%. Sequencing proved advantageous in comparison to the cultivation mainly in case of highly diverse microbial communities, where we could additionally detect numerous obligate and facultative anaerobic bacteria from genera Anaerococcus, Finegoldia, Porphyromonas, Morganella, and Providencia. Comparing swabs and biopsy tissues we concluded, that neither sampling method shows significant advantage over the other regardless of the method used (16S-AS or cultivation). In this study, chronic wound microbiota could be distributed into three groups based on the bacterial community diversity. The chronic wound surface area was positively correlated with bacterial diversity in swab specimens but not in biopsy tissues. Larger chronic wound surface area was also associated with the presence of Pseudomonas in both biopsy and swab specimens. The presence of Corynebacterium species at the initial visit was the microbial marker most predictive of the unfavorable clinical outcome after one-year follow-up visit.Entities:
Keywords: 16S amplicon sequencing; Corynebacterium; biopsy; chronic wound; cultivation; swab; wound microbiology
Year: 2021 PMID: 34150786 PMCID: PMC8211761 DOI: 10.3389/fmed.2021.607255
Source DB: PubMed Journal: Front Med (Lausanne) ISSN: 2296-858X
Figure 1Concordance in the detection of bacterial species (cultivation) or genera (16S-AS) in swabs and biopsy specimens obtained from chronic wounds. Colors in the frequency histograms denote the percentages of samples according to the matching/non-matching detections between swab/biopsy sample pairs of the same CW. Results are presented for cultivation-based approach (A) and 16S-AS (B), separately. Venn diagrams show cumulative percentages for all detected bacterial groups. Note that (A) (cultivation) represent diversity at the species taxonomic level while (B) (16S-AS) at the genus taxonomic level, therefore the direct comparison of detectable diversity between methods is not possible in this figure.
Figure 2Concordance in the detection of bacterial genera with cultivation and 16S-AS in chronic wounds. Heat-plots show relative abundances of bacterial genera across all analyzed CW samples obtained from swabs (top) and biopsies (below). Red dots denote genera, which were also detected with cultivation-based approach. Samples were assigned to three diversity groups (A, B, and C), based on the number of operational taxonomic units (OTUs) that were required to cover 99% of total obtained sequencing reads. Diversity groups were not associated with the number of reads obtained per sample, indicated by the symbols shown above the heat-plots approximating the number of reads per sample into three categories. Histograms (right) show the concordance between cultivation-based detection and 16S-AS. Venn diagrams show cumulative percentages for all detected bacterial genera.
Figure 3Microbiota association with wound surface area at the time of sampling and clinical outcome at 1-year follow-up. (A) CW surface area was positively correlated with the Pseudomonas (OTU1) abundance (left), significant for both biopsy (blue) and swab specimens (red); and with a larger diversity of the bacterial community, but only in swab specimens (right). (B) Unfavorable clinical outcomes were most significantly associated with a larger CW surface area (left) and the clinically estimated presence of biofilm (right). Red lines/points denote group means.