Recently, growing attention has been directed worldwide toward antimicrobial-resistant (AMR) bacterial pathogens. The infections caused by multidrug-resistant bacteria were declared a 'silent pandemic' due to increased patient morbidity and mortality. To combat such infections, specialists in various fields need to work together, which will ensure a better understanding of the mechanisms driving resistance dissemination.The resistance spreading in bacteria is driven by several lineages called 'global clones', the surveillance of which is an important task. Monitoring of AMR gene presence within samples of various origins is essential for tracking resistance acquisition and developing control measures within the scope of the One Health paradigm. Currently, molecular and whole-genome sequencing (WGS)-based methods are the gold standard for global clone detection and investigation of the pathogenicity factors in bacteria. This collection describes various applications of molecular biology, WGS, and genomic epidemiology methods for investigating bacterial pathogens, with a focus on population structure and AMR gene detection, and highlights the importance of genomic epidemiology methods for studying the clonal structure and AMR gene content of bacteria from various sources. The data provided will be useful for researchers in various fields involving bacterial pathogen surveillance, detection, and treatment, especially in the emerging field of genomic epidemiology.