title: One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers.
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.
authors.affiliation: School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE, UK.
authors.forename: Karen
authors.initials: K
authors.lastname: Smith
authors.affiliation: NHS Ayrshire and Arran, University Hospital Ayr, Ayr, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Collier
authors.affiliation: School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE, UK.|Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
authors.forename: Eleanor M
authors.initials: EM
authors.lastname: Townsend
authors.affiliation: Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
authors.forename: Lindsay E
authors.initials: LE
authors.lastname: O'Donnell
authors.affiliation: NHS Ayrshire and Arran, University Hospital Ayr, Ayr, UK.
authors.forename: Abhijit M
authors.initials: AM
authors.lastname: Bal
authors.affiliation: School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE, UK.
authors.forename: John
authors.initials: J
authors.lastname: Butcher
authors.affiliation: School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE, UK.
authors.forename: William G
authors.initials: WG
authors.lastname: Mackay
authors.affiliation: Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. gordon.ramage@glasgow.ac.uk.
authors.forename: Gordon
authors.initials: G
authors.lastname: Ramage
authors.affiliation: School of Health, Nursing and Midwifery, Institute of Healthcare Associated Infection, University of the West of Scotland, Barbour Building, Paisley Campus, Paisley, PA1 2BE, UK.
authors.forename: Craig
authors.initials: C
authors.lastname: Williams
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000693:Anaerobiosis; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D017719:Diabetic Foot / Q000382:microbiology*; D005260:Female; D006801:Humans; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D025341:Principal Component Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: 16S amplicon sequencing; Diabetes; Diabetic foot ulcer; Infection; Microbiome; Next generation sequencing