Nanopore metagenomics of plague-focus soils in Ulanqab Plateau, Inner Mongolia: microbial communities, antibiotic resistance, and pathogen-host interactions

Plague, caused by Yersinia pestis, persists as a significant zoonotic disease with complex environmental reservoirs. In this study, we applied third-generation Oxford Nanopore Technology (ONT) R10 sequencing to conduct the first comprehensive metagenomic analysis of soils from natural plague foci in the Ulanchab Plateau, Inner Mongolia. High-throughput long-read sequencing enabled detailed characterization of soil microbial communities, revealing dominance by Actinobacteria, Acidobacteria, and Proteobacteria, with observed compositional variations. Functional annotation indicated diverse metabolic capabilities, particularly in amino acid and carbohydrate metabolism, energy production, and environmental adaptation. Notably, a rich array of antibiotic resistance genes (ARGs) was detected, with vancomycin resistance genes most prevalent, alongside multidrug, aminoglycoside, and methotrexate resistance genes. Pathogen-host interaction (PHI) gene analysis focused specifically on PHI genes annotated to the Y. pestis species, with genes showing homology to genes including BipA and ZnuC abundant. Although Y. pestis was not detected by metagenomics or qPCR, the presence of Y. pestis-associated PHI gene fragments suggests potential for pathogen persistence. These findings demonstrate that plague-endemic soils are dynamic reservoirs of resistance and virulence determinants, underscoring the value of advanced long-read metagenomics for environmental pathogen surveillance and risk assessment.