Insights into polymicrobial communities in wound infections

Delayed wound healing, particularly in patients with comorbidities like diabetes, represents a significant health and economic burden, often resulting in a reduced quality of life for these patients. Infection is a key factor in delayed wound healing, with antimicrobial resistance a confounding issue in treatment regimens. Traditional culture-based methods primarily identify predominant pathogens, overlooking the complex wound microbiota, which can influence healing and treatment outcomes. This project explored the dynamics of mixed microbial communities and their antibiotic resistance profiles in both laboratory and clinical settings. An in vitro model revealed that mixed bacterial communities can protect susceptible strains from antibiotics, with the extent of this protection varying by antibiotic concentration and bacterial lifestyle (planktonic versus biofilm). The study also optimised host DNA depletion and DNA extraction methods to better analyse the wound microbiome. A 5% saponin-based method significantly reduced human DNA contamination in wound samples (p<0.0001), enhancing bacterial detection and increasing the number of unique species identified. This method was then applied in a longitudinal study of the microbiome of diabetic foot ulcers (DFUs). Over five weeks, wound swabs were collected, and the microbiome was analysed using Nanopore sequencing. Key bacteria like Staphylococcus aureus, Corynebacterium striatum, and Finegoldia magna were identified, alongside a comprehensive microbiome profile and associated antibiotic resistance genes. The study revealed that culture-based diagnostics often miss low-abundance species or overlook certain species, underscoring the need to consider the entire microbial community rather than just commonly culturable pathogens. The findings highlight the importance of advanced molecular techniques in understanding wound microbiota dynamics and resistance profiles. This study challenges the traditional focus on dominant pathogens and highlights the necessity of considering the entire microbial community. Overall, the data presented in this thesis offers insights into the complex microbial communities in wound infections, with implications for future microbiome studies, diagnostics and antibiotic treatment.