CliPME: The Clinical Pathogenic Bacteria Mutation and Expression Database

The ongoing battle between humans and pathogenic bacteria has fueled rapid microbial evolution. Although whole-genome sequencing technology (WGS) has transformed the ability to track genomic mutations, existing tools lack comprehensive solutions for analyzing mutational patterns and their functional consequences in pathogenic bacteria. Here, we present CliPME, an innovative platform that bridges this critical gap by combining mutation detection, mutation effect prediction, and regulatory network analysis specifically designed for bacterial genomics. We constructed qMut, a high-performance R package designed for large-scale mutation profiling. Coupled with three major functional modules called MutFinder, MutAnalyzer, and ExpMiner, the CliPME database integrates population-level mutation analysis, functional mutation predictions, and gene-gene expression relationships estimation. Using Mycobacterium tuberculosis (Mtb) as a case study, we demonstrated the power of the CliPME database by revealing functionally significant mutations in the transcription factor Rv0324 , and experimentally demonstrated the link of its genetic variation to possible adaptive phenotypes. This resource empowers researchers to decode evolutionary mechanisms in bacterial pathogens and may accelerate the translation of genomic insights into novel antimicrobial strategies. The web server of the CliPME is freely accessible at http://www.clipme.top:11725/.