The progressive increase of antibiotic resistance poses an alarming threat on public health worldwide. Although antibiotic resistance is a problem of human health, a one health approach to tackling antibiotic resistance is required, due to the effect of animal and environment on human health. To exactly estimate the impact of animal and environment on the spread of antibiotic resistance in human, scientific evidence with high quality is required. Molecular analysis of antibiotic-resistant bacteria through high-resolution, such as whole-genome sequencing, is suitable for obtaining credible evidence in examining the transmission of strains or genetic mobile elements responsible for antibiotic resistance among human, animal, and environment. In this paper, we discuss many observational studies using the whole-genome sequencing on various isolates collected from human, animal, and environment. These analyses suggest that more extensive surveillance based on whole-genome sequencing is required to accurately assess the potential threat of animal and environment on the spread of antibiotic resistance in human and that the effort to overcome various limitations in obtaining higher quality evidence is required.