A Survey of the Microbiome, Culturome and ARG Profile of a Cohort of Chronic Diabetic Foot Lesions

This study aimed to analyse the microbiome of chronic infected diabetic foot ulcers (DFUs) using parallel methods: traditional culture (the culturome), 16S rRNA gene sequencing (the microbiome) as well as the Antibiotic Resistance Gene (ARG) profile of isolated strains. Swab samples were collected in parallel from affected ulcers. The microbiome sequencing results identified that all patients had a polymicrobial flora with the five most frequent genus level OTUs as Escherichia, Staphylococcus, Streptococcus, Pseudomonas and the anaerobe Anaerococcus. Microbiological culture from the same swabs identified multiple species in all but two patient samples and revealed the most common isolates as CoNS Staphylococcus (17%), Enterococcus faecalis (14.3%), Corynebacterium spp. (10.7%), Anaerococcus spp. (7%), Staphylococcus aureus (8%) and Pseudomonas aeruginosa (6%). Enteric pathogens such as Klebsiella spp. were also frequently isolated. Attempts to revive anaerobes were largely unsuccessful, identifying a limitation in clinical microbiology storage protocols. Genome sequencing of 55 isolates revealed a high number of ARGs relating to β-lactams and tetracyclines, indicating multi-drug-resistant organisms (MDROs). This was confirmed by phenotypic antimicrobial susceptibility data that included several highly resistant Gram-negative bacteria. Overall, our data add to the picture of DFU microbiome as complex and displaying high levels of anti-microbial resistance (AMR).