Characterisation of the wound microbiome and antimicrobial resistance profiles in clinical isolates from epidermolysis bullosa patients

Epidermolysis bullosa (EB) encompasses a rare, inherited group of skin disorders characterised by skin fragility, leading to painful, chronic wounds. While recent international studies have reported reduced microbial diversity and altered bacterial composition in EB blistered skins, no microbiome or antimicrobial resistance data is available for Australian EB patients. The objectives of this study were to characterise the wound microbiome of Australian EB patients and identify bacterial pathogens and their associated antimicrobial resistance profiles. A total of 15 chronic wound swabs were collected from 10 EB patients. Bacterial identification was performed using standard culture methods and MALDI-TOF; for a selected resistant subset, whole-genome sequencing (WGS) was conducted on two strains, and full-length 16S rRNA gene sequencing was performed on 10 swab samples. Antimicrobial susceptibility profiles were determined using disk diffusion assays. PacBio Full-length 16S rRNA sequence analysis revealed a high relative abundance of the genera Staphylococcus and Streptococcus, with Staphylococcus aureus being the most frequently detected species. Among the 27 cultured bacterial isolates, 81.5% exhibited resistance to at least one antibiotic, and 22.2% were classified as multidrug resistance (MDR). WGS of two selected resistant strains harboured blaZ, mecA, ermC and mupA genes conferring resistance to penicillins, cefoxitin, clindamycin and high-level mupirocin, respectively. This is the first study to profile the wound microbiome and antimicrobial resistance in Australian EB patients. The findings provide the descriptive microbial profiles and resistance patterns, with implications for clinical management of patients in a specific healthcare setting.