Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing
Open accessAbstract
Background: Chronic wounds affect millions of people and cost billions of dollars in the United States each year. These wounds harbor polymicrobial biofilm communities, which can be difficult to elucidate using culturing methods. Clinical molecular microbiological methods are increasingly being employed to investigate the microbiota of chronic infections, including wounds, as part of standard patient care. However, molecular testing is more sensitive than culturing, which results in markedly different results being reported to clinicians. This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing), and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture. Methods: Parallel samples from 51 chronic wounds were studied using aerobic culturing and 16S DNA sequencing for the identification of bacteria. Results: One hundred forty-five (145) unique genera were identified using molecular methods, and 68 of these genera were aerotolerant. Fourteen (14) unique genera were identified using aerobic culture methods. One-third (31/92) of the cultures were determined to be < 1% of the relative abundance of the wound microbiota using molecular testing. At the genus level, molecular testing identified 85% (78/92) of the bacteria that were identified by culture. Conversely, culturing detected 15.7% (78/497) of the aerotolerant bacteria and detected 54.9% of the collective aerotolerant relative abundance of the samples. Aerotolerant bacterial genera (and individual species including Staphylococcus aureus , Pseudomonas aeruginosa , and Enterococcus faecalis ) with higher relative abundance scores were more likely to be detected by culture as demonstrated with regression modeling. Conclusion: Discordance between molecular and culture testing is often observed. However, culture-free 16S ribosomal DNA sequencing and its relative abundance score can provide clinicians with insight into which bacteria are most abundant in a sample and which are most likely to be detected by culture.
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Identification of particular polymicrobial organisms or observation of high protease levels such as MMPs or ADAMs in the wound bed are already being used to modify treatment plans and improve outcomes.
“The identification of particular polymicrobial organisms (179) or the observation of high protease levels, such as MMPs or ADAMs (a disintegrin and metalloproteinases), found in the wound bed (180) are already being used to modify treatment plans and improve outcomes.”
From Wound repair and regeneration: Mechanisms, signaling, and translation (2014) · cites this paper as [179]
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- Authors
- Rhoads, D. D., Cox, S. B., Rees, E. J., Sun, Y., & Wolcott, R. D.
- Affiliations
- University of Pittsburgh Medical Center (US)
- Southwest Regional Wound Care Center (US)
- Corresponding author
- Wolcott, Randall D
- Venue
- BMC Infectious Diseases
- Published
- 2012-11-24
- Volume
- 12
- Issue
- 1
- Pages
- 321-321
- ISSN
- 1471-2334 (ISSN-L)
- PMC
- PMC3542000
- OpenAlex
- W2115171049
- Cited by
- 167
- References
- 17
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 15 · 2023: 15 · 2022: 11 · 2021: 15 · 2020: 12 · 2019: 19 · 2018: 15 · 2017: 14 · 2016: 10 · 2015: 11 · 2014: 13 · 2013: 6
- FWCI
- 6.16
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Infectious Diseases (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- D-Scholarship@Pitt (University of Pittsburgh) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Health Sciences › Medicine › Rehabilitation › Wound Healing and Treatments
- Health Sciences › Medicine › Microbiology › Actinomycetales infections and treatment
- Keywords
- chronic wound infection, wound microbiota, polymicrobial biofilms, Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis, bacterial identification
- MeSH terms
- Bacteria, Bacterial Infections, Bacteriological Techniques, Chronic Disease, DNA, Ribosomal, Humans, RNA, Ribosomal, 16S, United States, Wound Infection, Molecular Diagnostic Techniques
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