Lesion Associated Bacterial Dysbiosis in Patients with Cutaneous Leishmaniasis in Ethiopia

Background: Cutaneous leishmaniasis (CL) is a chronic skin disease frequently complicated by bacterial superinfection and poor treatment outcomes. Lesion-associated bacterial dysbiosis may contribute to inflammation and impaired healing, but sequencing studies have not included African populations and have mainly involved adults. We characterised the skin microbiome of patients with CL in Ethiopia.

Methods: In this community-based cross-sectional study in southern Ethiopia, lesion and matched contralateral healthy-skin swabs were collected from clinically diagnosed patients and analysed by 16S rRNA V3–V4 amplicon sequencing. Alpha diversity, beta diversity, and taxonomic composition were compared between paired samples; associations with clinical characteristics were explored.

Findings After quality control, 88 samples from 47 patients were retained, including 41 lesion–healthy skin pairs. Thirty-two (68%) patients were younger than 14 years. Lesions had lower observed richness, Shannon diversity, and Simpson diversity than healthy skin (all p<0·0001). Community composition differed modestly (PERMANOVA R²=0·065, p=0·001), although dispersion also differed (PERMDISP p=0·036). Staphylococcaceae and Streptococcaceae each comprised more than 25% of the bacterial community in 16 (39%) and 14 (34%) lesions, respectively. No clear associations were found with lesion characteristics or previous traditional treatment.

Interpretation: The consistent reduction in bacterial diversity and enrichment of opportunistic taxa across endemic settings suggest that lesion-associated dysbiosis is a recurring feature of cutaneous leishmaniasis. These findings extend current evidence to an African and predominantly paediatric population and support investigating whether the skin microbiome contributes to lesion persistence or could be targeted alongside antileishmanial treatment.