Succession and ecology of diabetic foot ulcers biofilms

Abstract

Diabetic foot ulcers (DFU) are a common complication for patients with diabetes; these wounds are often complicated by complex microbial communities that colonize the wound, subsequently forming biofilms, and causing acute and chronic infections that prove hard to treat. Identifying key taxa contributing to pathogenesis, biofilm formation, and delayed wound healing is an area of interest for researchers in the field. However, understanding the ecological principles behind community assembly associated with biofilm formation is a relatively unexplored area of research. This thesis utilizes both 16s rDNA and whole genome shotgun sequencing to investigate the role of succession in biofilm community assembly within the DFU microbiome. Five patient isolates were grown on Cutimed Sorbact, alongside a number of lab strains; this enabled the observation that Sorbact is a suitable medium to capture the biofilm forming community on a clinical DFU. A clinical time series was conducted, sampling the wound microbiome of a patient with a chronic DFU over 72 hours. 16s rDNA and Whole genome shotgun sequencing was then completed on the time series and analysed using Qiime2 and BV-Brc respectively. The Qiime2 analysis identified a number of high abundance genera, composed of typical DFU isolates alongside a handful of novel genera (Pasteurella and Helcococcus). Community shifts were observed, similar to findings in previous succession models. Genome annotation identified two of the patient isolates (Pseudomonas aeruginosa and Enterococcus faecalis), both of which had a suite of virulency, antibiotic resistance, and biofilm forming genes. Annotation of the clinical time series revealed Pasteurella multocida to have a suite of virulence and biofilm associated genes - suggesting it was the main biofilm former; whilst the other species detected had few virulence or biofilm associated genes, likely being colonisers of the mature biofilm. In conclusion, the community shifts observed were concurrent with the annotated genomes, suggesting bystander/coloniser taxa filled niches once the biofilm matured in a succession like manner. However, further investigation with a larger sample size, and increased sequence depth is necessary to substantiate these findings.

Date of Award	2023
Original language	English
Awarding Institution	Western Sydney University
Supervisor	Thomas Jeffries (Supervisor)