The microbiome enhances transcriptional inflammatory signatures and delays clinical resolution in cutaneous leishmaniasis

Abstract

Abstract Cutaneous leishmaniasis (CL) is a protozoal infection in which the immune response plays a major role in lesion development. The activation of local responses such as cytolysis by CD8+ T cells and release of IL-1β by myeloid cells is associated with poor clinical outcome in patients. We found that lesions from cutaneous leishmaniasis patients also exhibit a bacterial dysbiosis, but whether this dysbiosis affects immune responses and consequently impacts chemotherapy to heal the patients is unknown. We carried out an integrative multi-omics analysis of 64 patients, including RNA-seq and 16S-seq from lesion biopsies and clinical metadata. Staphylococcus was the dominant overrepresented genus in lesions from most patients, so we generated an in-house S. aureus pangenome to quantify transcript abundances through dual RNA-seq mapping analysis. Increased overall bacterial burden assessed by qPCR and the presence of S. aureus assessed by dual RNA-seq indicated enrichment for cytokines (e.g., IL1B), inflammatory responses (e.g., PTGS2), and chemotaxis (e.g., CXCL8) by Gene Ontology analysis. Of particular importance, we found that lesions with increased S. aureus transcript abundances exhibited high expression of inflammatory-related genes that have been associated with treatment failure, such as PRF1, GNLY, and GZMB. Correspondingly, we found that patients with a Staphylococcus spp. dysbiosis exhibited a delay in resolving their lesions following treatment. These results indicate that the microbiome influences the local immune responses in CL, affecting how patients respond to therapy by delaying the healing time. These results suggest that the use of antibiotics combined with chemotherapy may improve treatment outcome for CL. Supported by grant from NIH (R01 AI149456)