Pt5e, a mutant peptide derived from the C-terminal 55 residues of zebrafish phosvitin, has been suggested to be a novel antibacterial peptide. However, if it is applicable to clinical MDR bacteria remains to be tested. In this study, high-purity Pt5e was first expressed and purified by fusion with cationic elastin-like polypeptide. Pt5e was then shown to be capable of effectively killing all the five clinical MDR bacteria tested. Pt5e kill the MDR bacteria at several levels, including inserting into the bacterial membranes, causing the membrane depolarization and permeabilization, and inducing the intracellular apoptosis/necrosis. All these data suggest that Pt5e is a promising therapeutic potential as an antibiotics against clinical MDR bacteria.