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

Aims To conduct the first comprehensive metagenomic analysis of soils from natural plague foci in the Ulanqab Plateau, Inner Mongolia, characterizing the soil microbial communities, profiling the diversity and abundance of antibiotic resistance genes (ARGs), and identifying pathogen-host interaction (PHI) genes with homology to Yersinia pestis. Methods and Results We applied third-generation Oxford Nanopore Technology (ONT) R10 sequencing to soil samples collected from two historic plague foci. High-throughput long-read sequencing enabled detailed characterization of soil microbial communities, functional annotation, and detection of ARGs and PHI genes. The microbial community was dominated by Actinobacteria, Acidobacteria, and Proteobacteria. Functional annotation indicated diverse metabolic capabilities, particularly in amino acid and carbohydrate metabolism. A rich array of ARGs was detected, with vancomycin resistance genes being most prevalent. PHI gene analysis focused specifically on genes annotated to the Y. pestis species revealed abundant homologs of BipA and ZnuC. Although Y. pestis was not detected by metagenomics or qPCR, the presence of Y. pestis-associated PHI gene fragments suggests potential for pathogen persistence. Conclusions Plague-endemic soils in the Ulanqab Plateau are dynamic reservoirs of resistance and virulence determinants. The findings demonstrate the value of advanced long-read metagenomics for environmental pathogen surveillance and risk assessment, highlighting the ecological complexity of these environments and their potential role in maintaining antibiotic resistance and virulence genes.