The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing

Travis, Jason; Malone, Matthew; Hu, Honghua; Baten, Abdul; Johani, Khalid; Huygens, Flavia; Vickery, Karen; Benkendorff, Kirsten

doi:10.1186/s12866-020-01843-2

Cited by 29 publications

(35 citation statements)

References 52 publications

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“…sequencing was particularly useful for detecting pathogens that are difficult or impossible to cultivate, especially when antibiotics were given before sample acquisition. This was in line with previous studies that showed that 16S sequencing is more sensitive than culture studies for pathogen detection in DFIs (1,3,26,27). Moreover, in most DFIs, antibiotics are prescribed before the debridement surgery (28-30), which would be another reason for the lower diagnostic yield of the culture studies (31)(32)(33).…”

Section: Discussionsupporting

confidence: 87%

Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections

et al. 2021

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Diabetic foot infections (DFIs) cause substantial morbidity and mortality. The mainstay of the treatment is empiric antibiotics and surgical debridement in severe cases. In this study, we performed nanopore 16S rDNA sequencing from the debridement specimens of DFIs. Fifty-four surgical debridement specimens obtained from 45 patients with medically intractable DFI were included. The 16S rDNA PCR was performed on each specimen, and Nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database, and the results were compared with conventional culture studies. The 16S sequencing results revealed that the majority of the DFIs (44 of 54, 81.5%) were polymicrobial infections. All bacteria isolated by conventional culture studies were detected by 16S sequencing. Several anaerobes (Prevotella, Finegoldia, Anaerococcus, Bacteroides) were commonly identified by 16S sequencing but were frequently missed by culture studies. In many cases, certain bacteria only revealed by the 16S sequencing were more abundant than the bacteria isolated by the culture studies. In conclusion, nanopore 16S sequencing was capable of pathogen identification in DFIs and has many advantages over conventional culture studies. Nanopore 16S sequencing enables a comprehensive understanding of the bacteria involved in DFIs.

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Section: Discussionsupporting

confidence: 87%

Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections

et al. 2021

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“…Our rationale for using wound swabs in this study is supported from recent evidence identifying that wound swabs from DFUs using the Levine method were found to effectively detect bacteria at a similar or higher frequency to those recovered from tissue biopsy samples when using 16S rRNA sequencing. 30 …”

Section: Discussionmentioning

confidence: 99%

Efficacy of a topical concentrated surfactant gel on microbial communities in non‐healing diabetic foot ulcers with chronic biofilm infections: A proof‐of‐concept study

Malone

Radzieta

Schwarzer

et al. 2021

International Wound Journal

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This proof-of-concept study sought to determine the effects of standard of care (SOC) and a topically applied concentrated surfactant gel (SG) on the total microbial load, community composition, and community diversity in nonhealing diabetic foot ulcers (DFUs) with chronic biofilm infections. SOC was provided in addition to a topical concentrated SG, applied every 2 days for 6 weeks. Wound swabs were obtained from the base of ulcers at baseline (week 0), week 1, mid-point (week 3), and end of treatment (week 6). DNA sequencing and real-time quantitative polymerase chain reaction (qPCR) were employed to determine the total microbial load, community composition, and diversity of patient samples. Tissue specimens were obtained at baseline and scanning electron microscopy and peptide nucleic acid fluorescent in situ hybridisation with confocal laser scanning microscopy were used to confirm the presence of biofilm in all 10 DFUs with suspected chronic biofilm infections. The application of SG resulted in 7 of 10 samples achieving a reduction in mean log10 total microbial load from baseline to end of treatment (0.8 Log10 16S copies, ±0.6), and 3 of 10 samples demonstrated an increase in mean Log10 total microbial load (0.6 log10 16S copies, ±0.8) from baseline to end of treatment. Composition changes in microbial communities were driven by changes to the most dominant bacteria. Corynebacterium sp. and Streptococcus sp. frequently reduced in relative abundance in patient samples from week 0 to week 6 but did not disappear. In contrast, Staphylococcus sp., Finegoldia sp., and Fusobacterium sp., relative abundances frequently increased in patient samples from week 0 to week 6. The application of a concentrated SG resulted in varying shifts to diversity (increase or decrease) between week 0 and week 6 samples at the individual patient level. Any shifts in community diversity were independent to changes in the total microbial loads. SOC and a topical concentrated SG directly affect the microbial loads and community composition of DFUs with chronic biofilm infections.

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“…Further, Travis et al found there was minimal correlation between the number and types of bacteria found in swabs compared to tissue biopsies. They also found tissue biopsies contained an overall greater diversity of bacterial species but that the frequency of potential pathogens was higher in wound swabs (50). While biopsies represent the gold standard to capture the true diversity of bacteria found in skin and wound samples, it is invasive and requires a skilled clinician.…”

Section: Methodologies For Characterizationmentioning

confidence: 99%

Biofilm-Innate Immune Interface: Contribution to Chronic Wound Formation

et al. 2021

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Delayed wound healing can cause significant issues for immobile and ageing individuals as well as those living with co-morbid conditions such as diabetes, cardiovascular disease, and cancer. These delays increase a patient’s risk for infection and, in severe cases, can result in the formation of chronic, non-healing ulcers (e.g., diabetic foot ulcers, surgical site infections, pressure ulcers and venous leg ulcers). Chronic wounds are very difficult and expensive to treat and there is an urgent need to develop more effective therapeutics that restore healing processes. Sustained innate immune activation and inflammation are common features observed across most chronic wound types. However, the factors driving this activation remain incompletely understood. Emerging evidence suggests that the composition and structure of the wound microbiome may play a central role in driving this dysregulated activation but the cellular and molecular mechanisms underlying these processes require further investigation. In this review, we will discuss the current literature on: 1) how bacterial populations and biofilms contribute to chronic wound formation, 2) the role of bacteria and biofilms in driving dysfunctional innate immune responses in chronic wounds, and 3) therapeutics currently available (or underdevelopment) that target bacteria-innate immune interactions to improve healing. We will also discuss potential issues in studying the complexity of immune-biofilm interactions in chronic wounds and explore future areas of investigation for the field.

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The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing

Cited by 29 publications

References 52 publications

Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections

Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections

Efficacy of a topical concentrated surfactant gel on microbial communities in non‐healing diabetic foot ulcers with chronic biofilm infections: A proof‐of‐concept study

Biofilm-Innate Immune Interface: Contribution to Chronic Wound Formation

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