Introduction
Diabetic foot ulcers (DFUs) are an increasingly common problem in diabetic patients. . Every three hours, someone in Australia loses a lower limb as a direct result of diabetes-related foot disease. It has been hypothesized that the microbiome of DFUs is a contributing factor in delayed wound healing. Very little is known about the presence and shifts in microorganisms that occur over time that are associated with DFU. This study examines the microbial diversity and abundance associated with DFUs using genome based methods.
Methods
Two diabetic patient cohorts (n=58 patients) with foot ulcers were studied over a period of 12-24 weeks. Genomic DNA (gDNA) was extracted from patient swab samples (n=362) and amplicon libraries were constructed targeting the V1 and V2 region of the prokaryotic 16S rRNA gene. The Ion Torrent Personal Genome Machine (PGM) was used for amplicon sequencing and the bioinformatics pipeline “mothur” was used to perform a quality control and analysis of the sequences obtained. Statistics and data visualisation was performed using Calypso.
Results
Approximately 6,416,041 high-quality sequences, with an average of 29,704 sequences per sample were generated. Sequencing analysis revealed differences in the microbiome composition of healing and non-healing DFUs as the abundance of some bacterial genera was statistically significant (p<0.05) in non-healing DFUs and vice versa.
Conclusion
This study suggests that the significant differential abundance of certain bacterial genera in chronic DFUs can be used as biomarkers to inform ulcer outcome and can inform the use of selective and appropriate antimicrobials. A greater understanding of the diabetic foot ulcer microbiome will help guide new treatment strategies to effectively control the infection and promote healing. This will in turn benefit patients suffering from these ulcers and improve their quality of life.