The present invention offers a solution to the lack of effective alternative treatments to fight infectious disease, preferably involving sepsis, comprising active ingredients obtained by non-intrusive and efficient methods. In particular, the present invention is the first to show that mesenchymal stem cells obtained from menstrual fluids (MenSCs) have the capacity to control infectious diseases, especially those leading to a reaction of the host body like sepsis. As shown herein, in vivo experiments illustrate that MenSCs have antibacterial activity in vitro, increase the survival rates of a mouse model for sepsis, regulate several parameters that are altered in sepsis patients and that are related with multi-organ dysfunction, such as the levels of Alanine aminotransferase (ALT), Aspartate aminotransferase (AST), alkaline phosphatase (ALP), glucose in blood, serum albumin, lung injury. Results show that in the mouse model for sepsis, MenScs also regulate the pro- and anti-inflammatory cytokine levels, reduce the loss of lymphocytes during sepsis and systemic bacterial proliferation in blood. The conditioned medium of MenSCs also increases the survival rates of mouse animals affected by sepsis. Overall, the invention offers a promising alternative method to treat infectious diseases. Since it is principally composed of stem cells present in menstrual fluid, the invention provides an ease access and repeated sampling in a non-invasive manner. Such attributes allow the rapid production of the treatment.