In this investigation, metal nanoparticles (NPs) have been used as antibiotics to inhibit the growth of bacteria. Here, we report an antibacterial study of ZnO-NPs, Co-NPs, and Au-NPs towards the approach for detecting the pathogenic strain of Escherichia coli (E. coli) cells. The nanoparticle (NP) acts as the detector probe for both live and dead pathogenic E. coli cells. The aim is to investigate the antibacterial bio-activities of metal NPs and their mode of action against pathogenic bacteria on the whole cell. Antibacterial activities of NPs were assessed by the agar diffusion method quantitatively and the quality and quantity of E.coli cells extraction in the presence of nanoparticles (ZnO-NPs, Au-NPs, Co-NPs). The optimized concentration kills the pathogenic E. coli cells and hence shows the enrichment of cells. Results indicate the highly efficient nanoparticles inhibit the growth of such pathogenic microorganisms. Nanoparticle metal oxides signify a novel course of vital materials that are progressively being advanced for use in research and health-related applications. At the same time, we use Raman spectroscopy and fluorescence microscopic images for a better understanding of the effect of NPs on bacterial cells.