One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers

Karen Smith, Andrew Collier, Eleanor Townsend, Lindsay O’Donnell, Abhijit Bal, John Butcher, William MacKay, Gordon Ramage, Craig Williams

Research output: Contribution to journalArticle

Abstract

Background
The aim of this study was to characterise the microbiome of new and recurrent diabetic foot ulcers using 16S amplicon sequencing (16S AS), allowing the identification of a wider range of bacterial species that may be important in the development of chronicity in these debilitating wounds. Twenty patients not receiving antibiotics for the past three months were selected, with swabs taken from each individual for culture and 16S AS. DNA was isolated using a combination of bead beating and kit extraction. Samples were sequenced on the Illumina Hiseq 2500 platform.

Results
Conventional laboratory culture showed positive growth from only 55 % of the patients, whereas 16S AS was positive for 75 % of the patients (41 unique genera, representing 82 different operational taxonomic units (OTU’s). S. aureus was isolated in 72 % of culture-positive samples, whereas the most commonly detected bacteria in all ulcers were Peptoniphilus spp., Anaerococcus spp. and Corynebacterium spp., with the addition of Staphylococcus spp. in new ulcers. The majority of OTU’s residing in both new and recurrent ulcers (over 67 %) were identified as facultative or strict anaerobic Gram-positive organisms. Principal component analysis (PCA) showed no difference in clustering between the two groups (new and recurrent ulcers).

Conclusions
The abundance of anaerobic bacteria has important implications for treatment as it suggests that the microbiome of each ulcer “starts afresh” and that, although diverse, are not distinctly different from one another with respect to new or recurrent ulcers. Therefore, when considering antibiotic therapy the duration of current ulceration may be a more important consideration than a history of healed ulcer.
Original languageEnglish
Article number54
JournalBMC Microbiology
Volume16
DOIs
Publication statusPublished - 22 Mar 2016

Fingerprint

Diabetic Foot
Microbiota
Ulcer
Bacteria
Anti-Bacterial Agents
Corynebacterium
Anaerobic Bacteria
Principal Component Analysis
Staphylococcus
Cluster Analysis
DNA
Wounds and Injuries
Therapeutics
Growth

Keywords

  • Diabetes
  • Diabetic foot ulcer
  • Infection
  • Microbiome
  • Next generation sequencing
  • 16S amplicon sequencing

Cite this

Smith, Karen ; Collier, Andrew ; Townsend, Eleanor ; O’Donnell, Lindsay ; Bal, Abhijit ; Butcher, John ; MacKay, William ; Ramage, Gordon ; Williams, Craig. / One step closer to understanding the role of bacteria in diabetic foot ulcers : characterising the microbiome of ulcers. In: BMC Microbiology. 2016 ; Vol. 16.
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title = "One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers",
abstract = "BackgroundThe aim of this study was to characterise the microbiome of new and recurrent diabetic foot ulcers using 16S amplicon sequencing (16S AS), allowing the identification of a wider range of bacterial species that may be important in the development of chronicity in these debilitating wounds. Twenty patients not receiving antibiotics for the past three months were selected, with swabs taken from each individual for culture and 16S AS. DNA was isolated using a combination of bead beating and kit extraction. Samples were sequenced on the Illumina Hiseq 2500 platform.ResultsConventional laboratory culture showed positive growth from only 55 {\%} of the patients, whereas 16S AS was positive for 75 {\%} of the patients (41 unique genera, representing 82 different operational taxonomic units (OTU’s). S. aureus was isolated in 72 {\%} of culture-positive samples, whereas the most commonly detected bacteria in all ulcers were Peptoniphilus spp., Anaerococcus spp. and Corynebacterium spp., with the addition of Staphylococcus spp. in new ulcers. The majority of OTU’s residing in both new and recurrent ulcers (over 67 {\%}) were identified as facultative or strict anaerobic Gram-positive organisms. Principal component analysis (PCA) showed no difference in clustering between the two groups (new and recurrent ulcers).ConclusionsThe abundance of anaerobic bacteria has important implications for treatment as it suggests that the microbiome of each ulcer “starts afresh” and that, although diverse, are not distinctly different from one another with respect to new or recurrent ulcers. Therefore, when considering antibiotic therapy the duration of current ulceration may be a more important consideration than a history of healed ulcer.",
keywords = "Diabetes, Diabetic foot ulcer, Infection, Microbiome, Next generation sequencing, 16S amplicon sequencing",
author = "Karen Smith and Andrew Collier and Eleanor Townsend and Lindsay O’Donnell and Abhijit Bal and John Butcher and William MacKay and Gordon Ramage and Craig Williams",
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One step closer to understanding the role of bacteria in diabetic foot ulcers : characterising the microbiome of ulcers. / Smith, Karen; Collier, Andrew; Townsend, Eleanor; O’Donnell, Lindsay ; Bal, Abhijit; Butcher, John; MacKay, William; Ramage, Gordon; Williams, Craig.

In: BMC Microbiology, Vol. 16, 54, 22.03.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - One step closer to understanding the role of bacteria in diabetic foot ulcers

T2 - characterising the microbiome of ulcers

AU - Smith, Karen

AU - Collier, Andrew

AU - Townsend, Eleanor

AU - O’Donnell, Lindsay

AU - Bal, Abhijit

AU - Butcher, John

AU - MacKay, William

AU - Ramage, Gordon

AU - Williams, Craig

PY - 2016/3/22

Y1 - 2016/3/22

N2 - BackgroundThe aim of this study was to characterise the microbiome of new and recurrent diabetic foot ulcers using 16S amplicon sequencing (16S AS), allowing the identification of a wider range of bacterial species that may be important in the development of chronicity in these debilitating wounds. Twenty patients not receiving antibiotics for the past three months were selected, with swabs taken from each individual for culture and 16S AS. DNA was isolated using a combination of bead beating and kit extraction. Samples were sequenced on the Illumina Hiseq 2500 platform.ResultsConventional laboratory culture showed positive growth from only 55 % of the patients, whereas 16S AS was positive for 75 % of the patients (41 unique genera, representing 82 different operational taxonomic units (OTU’s). S. aureus was isolated in 72 % of culture-positive samples, whereas the most commonly detected bacteria in all ulcers were Peptoniphilus spp., Anaerococcus spp. and Corynebacterium spp., with the addition of Staphylococcus spp. in new ulcers. The majority of OTU’s residing in both new and recurrent ulcers (over 67 %) were identified as facultative or strict anaerobic Gram-positive organisms. Principal component analysis (PCA) showed no difference in clustering between the two groups (new and recurrent ulcers).ConclusionsThe abundance of anaerobic bacteria has important implications for treatment as it suggests that the microbiome of each ulcer “starts afresh” and that, although diverse, are not distinctly different from one another with respect to new or recurrent ulcers. Therefore, when considering antibiotic therapy the duration of current ulceration may be a more important consideration than a history of healed ulcer.

AB - BackgroundThe aim of this study was to characterise the microbiome of new and recurrent diabetic foot ulcers using 16S amplicon sequencing (16S AS), allowing the identification of a wider range of bacterial species that may be important in the development of chronicity in these debilitating wounds. Twenty patients not receiving antibiotics for the past three months were selected, with swabs taken from each individual for culture and 16S AS. DNA was isolated using a combination of bead beating and kit extraction. Samples were sequenced on the Illumina Hiseq 2500 platform.ResultsConventional laboratory culture showed positive growth from only 55 % of the patients, whereas 16S AS was positive for 75 % of the patients (41 unique genera, representing 82 different operational taxonomic units (OTU’s). S. aureus was isolated in 72 % of culture-positive samples, whereas the most commonly detected bacteria in all ulcers were Peptoniphilus spp., Anaerococcus spp. and Corynebacterium spp., with the addition of Staphylococcus spp. in new ulcers. The majority of OTU’s residing in both new and recurrent ulcers (over 67 %) were identified as facultative or strict anaerobic Gram-positive organisms. Principal component analysis (PCA) showed no difference in clustering between the two groups (new and recurrent ulcers).ConclusionsThe abundance of anaerobic bacteria has important implications for treatment as it suggests that the microbiome of each ulcer “starts afresh” and that, although diverse, are not distinctly different from one another with respect to new or recurrent ulcers. Therefore, when considering antibiotic therapy the duration of current ulceration may be a more important consideration than a history of healed ulcer.

KW - Diabetes

KW - Diabetic foot ulcer

KW - Infection

KW - Microbiome

KW - Next generation sequencing

KW - 16S amplicon sequencing

U2 - 10.1186/s12866-016-0665-z

DO - 10.1186/s12866-016-0665-z

M3 - Article

VL - 16

JO - BMC Microbiology

JF - BMC Microbiology

SN - 1471-2180

M1 - 54

ER -