Next generation DNA sequencing of tissues from infected diabetic foot ulcers

M. Malone*, K. Johani, S. O. Jensen, I. B. Gosbell, H. G. Dickson, H. Hu, K. Vickery

*Corresponding author for this work

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

We used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on genomic analysis. Patients. ≥. 18. years presenting with a new Diabetic Foot Infection (DFI) who had not received topical or oral antimicrobials in the two weeks prior to presentation, were eligible for enrolment. Tissue punch biopsies were obtained from infected DFUs for analysis. Demographics, clinical and laboratory data were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (<. six weeks) all had one dominant bacterial species (n = 5 of 5, 100%, p. <. 0.001), Staphylococcus aureus in three cases and Streptococcus agalactiae in two. Longer duration DFUs (≥. six weeks) were diversely polymicrobial (p. <. 0.01) with an average of 63 (range 19-125) bacterial species. Severe DFIs had complex microbiomes and were distinctly dissimilar to less severe infections (p = 0.02), characterised by the presence of low frequency microorganisms. Nineteen patients (49%) during the study period experienced antimicrobial treatment failure, but no overall differences existed in the microbiome of patients who failed therapy and those who experienced treatment success (p = 0.2). Our results confirm that short DFUs have a simpler microbiome consisting of pyogenic cocci but chronic DFUs have a highly polymicrobial microbiome. The duration of a DFU may be useful as a guide to directing antimicrobial therapy.

Original languageEnglish
Pages (from-to)142-149
Number of pages8
JournalEBioMedicine
Volume21
DOIs
Publication statusPublished - Jul 2017

Keywords

  • 16S rRNA
  • Diabetic foot infections
  • Diabetic foot ulcers
  • Microbiome
  • Next generation DNA sequencing

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