Exploring DNA Methylation Patterns in the Core Genome of Klebsiella pneumoniae

In recent years, sequencing has become easily accessible and widespread, revolutionizing our ability to study complex genetic information. Thus, it is possible to analyze complex bacterial populations and investigate relationships between individual strains. Methods such as core genome multilocus sequence typing (cgMLST) are used in routine clinical practice to characterize bacterial isolates, track the spread of infectious diseases, and monitor outbreaks. However, the limitation lies in distinguishing closely related bacterial strains, which differ only in several bases. Therefore, here, we present the core genome methylome analysis utilizing nanopore sequencing. We demonstrate that epigenetic information contained within bacterial strains allows us to differentiate populations similarly to cgMLST. Moreover, the proposed unique combination of cgMLST with core genome methylome can even increase the discriminatory power between closely similar isolates, overcoming the constraints of cgMLST. Combining genomic and epigenomic information can provide better insight into bacterial strains’ evolution, transmission patterns and pathogenicity study.