Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds
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 characte...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-06-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2021.607255/full |
| _version_ | 1818591861160280064 |
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| author | Aleksander Mahnic Vesna Breznik Maja Bombek Ihan Maja Rupnik Maja Rupnik |
| author_facet | Aleksander Mahnic Vesna Breznik Maja Bombek Ihan Maja Rupnik Maja Rupnik |
| author_sort | Aleksander Mahnic |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-16T10:19:09Z |
| format | Article |
| id | doaj.art-32af2f9713004b149c83713989988a4a |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-12-16T10:19:09Z |
| publishDate | 2021-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Medicine |
| spelling | doaj.art-32af2f9713004b149c83713989988a4a2022-12-21T22:35:20ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2021-06-01810.3389/fmed.2021.607255607255Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic WoundsAleksander Mahnic0Vesna Breznik1Maja Bombek Ihan2Maja Rupnik3Maja Rupnik4National Laboratory for Health, Environment, and Food, Department for Microbiological Research, Maribor, SloveniaDepartment of Dermatology and Venereal Diseases, University Medical Centre Maribor, Maribor, SloveniaNational Laboratory for Health, Environment, and Food, Department for Medical Microbiology, Maribor, SloveniaNational Laboratory for Health, Environment, and Food, Department for Microbiological Research, Maribor, SloveniaDepartment of Microbiology, Faculty of Medicine, University of Maribor, Maribor, SloveniaChronic 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.https://www.frontiersin.org/articles/10.3389/fmed.2021.607255/fullchronic woundCorynebacteriumwound microbiology16S amplicon sequencingcultivationswab |
| spellingShingle | Aleksander Mahnic Vesna Breznik Maja Bombek Ihan Maja Rupnik Maja Rupnik Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds Frontiers in Medicine chronic wound Corynebacterium wound microbiology 16S amplicon sequencing cultivation swab |
| title | Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds |
| title_full | Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds |
| title_fullStr | Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds |
| title_full_unstemmed | Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds |
| title_short | Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds |
| title_sort | comparison between cultivation and sequencing based approaches for microbiota analysis in swabs and biopsies of chronic wounds |
| topic | chronic wound Corynebacterium wound microbiology 16S amplicon sequencing cultivation swab |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2021.607255/full |
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