247 23 Text: 4892 24 25 2 ABSTRACT Infections with Trypanosoma cruzi are usually life-long despite 26 generating a strong adaptive immune response. Identifying the sites of parasite 27persistence is therefore crucial to understand how T. cruzi avoids immune-mediated 28 destruction. However, this is a major technical challenge because the parasite burden 29 during chronic infections is extremely low. Here, we describe an integrated approach 30 involving comprehensive tissue processing, ex vivo imaging, and confocal 31 microscopy, which has allowed us to visualise infected host cells in murine tissue, with 32 exquisite sensitivity. Using bioluminescence-guided tissue sampling, with a detection 33 level of <20 parasites, we show that in the colon, smooth muscle myocytes in the 34 circular muscle layer are the most common infected host cell type. Typically, during 35 chronic infections, the entire colon of a mouse contains only a few hundred parasites, 36 often concentrated in a small number of cells containing >200 parasites, that we term 37 mega-nests. In contrast, during the acute stage, when the total parasite burden is 38 considerably higher and many cells are infected, nests containing >50 parasites are 39 rarely found. In C3H/HeN mice, but not BALB/c, we identified skeletal muscle as a 40 major site of persistence during the chronic stage, with most parasites found in large 41 mega-nests within the muscle fibres. Finally, we report that parasites are also 42 frequently found in the skin during chronic murine infections, often in multiple infection 43 foci. In addition to being a site of parasite persistence, this anatomical reservoir could 44 play an important role in insect-mediated transmission, and have implications for drug 45 development. 46 47 48 49 3 IMPORTANCE Trypanosoma cruzi causes Chagas disease, the most important 50 parasitic infection in Latin America. Major pathologies include severe damage to the 51 heart and digestive tract, although symptoms do not usually appear until decades after 52 infection. Research has been hampered by the complex nature of the disease and 53 technical difficulties in locating the extremely low number of parasites. Here, using 54 highly sensitive imaging technology, we reveal the sites of parasite persistence in 55 experimental mice at single-cell resolution. We show that parasites are frequently 56 located in smooth muscle cells in the circular muscle layer of the colon, and that 57 skeletal muscle cells and the skin can also be important reservoirs. This information 58 provides a framework for investigating how the parasite is able to survive as a life-long 59 infection, despite a vigorous immune response. It also informs drug-development 60 strategies by identifying tissue sites that must be accessed to achieve a curative 61 outcome.62 63 64 65 66 KEY WORDS: Trypanosoma cruzi, Chagas disease, chronic persistence, murine 67 imaging, colon, skeletal muscle, skin 68 69 70 71 72 73 74 4 INTRODUCTION The intracellular protozoan parasite Trypanosoma cruzi is the...