Living particles such as bacteria are able to transfer through membrane pores that are smaller than cell size due to the specific stiffness of this type of microorganism. This phenomenon can lead to a significant loss of selectivity in the filtration process, which is a major cause of concern in the sterilizing filtration step. This study investigates the retention of three bacteria strains: Escherichia coli CIP 54124, Pseudomonas aeruginosa CIP 103467 and Staphylococcus aureus CIP 53154 by model porous membranes for various operating conditions (transmembrane pressure, feed concentration and the physicochemical composition of filtered media with antibacterial agent added at sublethal concentration). The first part of this study is dedicated to defining the size and the nanomechanical properties of the envelope of the studied bacteria by microscopic techniques (Transmission electron microscopy & Atomic-force microscopy), in order to then explore the role of these quantifiable characteristics on the cell transfer through the pores by deformation mechanisms. Our results lead to the development of a numerical model to connect the observed retention efficiency of the filtration experiment and the microscopic information about individual particles.