Exploring the microbiome of Kyiv Metro and identifying antibiotic resistance genes using modern methods of metagenomics and bioinformatics

One of the pressing issues of today is the study of the microbiome of the urban environment due to the rapid acquisition of antibiotic resistance by pathogenic microbes, especially in public mass transit systems. Large-scale studies of microbial communities became possible with the development of sequencing technologies and metagenomics, a study of all genetic material in a given environment, which provides insight into its taxonomical and functional profiles. At the same time, locations in Kyiv have not been studied for pathogenic microorganisms using whole-genome sequencing. This work presents a metagenomic analysis of samples collected at five underground stations of the Obolonsko-Teremkivska line of the Kyiv subway. Microorganisms were taxonomically identified, along with the core microbiome and potentially pathogenic species, and antimicrobial resistance genes were screened. We found that the samples have a high overall homogeneity, and a core microbiome is formed mainly by taxa inherent to the human organism. Resistance genes were identified, the most common of which was qacG, probably associated with the use of disinfectants. The results of this work can significantly affect the understanding of how resistance genes spread, as well as contribute to further research into the environment of the city of Kyiv.