26Each year 700,000 to 1.2 million new cases of cutaneous leishmaniasis (CL) are reported 27 and yet CL remains one of thirteen diseases classified as neglected tropical diseases (NTDs). 28 Leishmania major is one of several different species of that same genus that can cause CL. 29 Current CL treatments are limited by adverse effects and rising resistance. Studying disease 30 metabolism at the site of infection can lead to new drug targets. In this study, samples were 31 collected from mice infected in the ear and footpad with L. major and analyzed by untargeted 32 liquid chromatography-tandem mass spectrometry (LC-MS/MS). Significant differences in 33 overall metabolite profiles were noted in the ear at the site of the lesion. Interestingly, lesion-34 adjacent, macroscopically healthy sites also showed alterations in specific metabolites, including 35 select phosphocholines (PCs). Host-derived PCs in the lower m/z range (m/z 200-799) showed an 36 increase with infection in the ear at the lesion site, while those in the higher m/z range (m/z 800-37 899) were decreased with infection at the lesion site. Overall, our results expanded our 38 understanding of the mechanisms of CL pathogenesis through the host metabolism and may lead 39 to new curative measures against infection with Leishmania. 40 Author summary 41 Cutaneous leishmaniasis (CL) is one of thirteen neglected tropical diseases in the world 42 today. It is an infectious disease with a wide distribution spanning five continents, with 43 increasing distribution expected due to climate change. CL manifests as skin lesions and ulcers 44 that are disabling and stigmatized. With the current treatment options being limited, studying 45 host-pathogen metabolism can uncover mechanisms of disease pathogenesis that may lead to 46 new curative measures against infection. In this paper we used untargeted metabolomics to 47 address molecular-level changes occurring in vivo in experimental skin lesions of Leishmania 48 major. Distinct global metabolic profiles were observed. Total phosphocholines (PCs) and those 49 in the lower m/z ranges were significantly higher at the site of the skin lesion in the ear. In 50 addition, specific PCs as well as PCs of varied m/z ranges were also affected at healthy-51 appearing lesion-adjacent sites, indicating that infection-induced metabolic perturbations are not 52 restricted to the lesion site. Ultimately, these results provide essential clues to the metabolic 53 pathways affected by CL. 54 Introduction 55 Leishmaniasis affects people in 88 countries worldwide in tropical, subtropical and 56 temperate regions, putting approximately 350 million individuals at risk of infection, with 57 approximately 12 million battling the disease [1]. It is one of the three most impactful vector-58 borne protozoan neglected tropical diseases, causing approximately 2.1 million DALYs 59 (Disability-Adjusted Life Years) and 51,000 deaths. With recent population movements, 60 leishmaniasis is now affecting people in non-endemic regions as wel...