Study On SNP Population Relationship Of Yersinia Pestis Genome Sequence In The Natural Foci Of Gerbil Plague In Inner Mongolia Autonomous Region In 2019

Objective There were frequent occurrences of plague among animals in the Inner Mongolia Autonomous Region in 2019,accompanied by the sporadic occurrence of human plague cases,which is a severe issue for the control of plague in Inner Mongolia.This study aimed at understanding the phylogenetic relationship of Yersinia pestis by aligning single nucleotide polymorphism(SNP)in the Inner Mongolian Meriones unguiculatus plague natural foci in 2019,further source tracing the possible origination of Y.pestis that isolated from plague patients in 2019.Methods A total of 135 Y.pestis nucleic acids were extracted from the Plague foci of Inner Mongolia Autonomous Region in 2018 and 2019.These strains include 18 isolates in 2018 and 117 isolates in 2019.Commercial sequencing obtained the genome sequence of 135 Yersinia pestis strains.Use population single nucleotide polymorphism(SNP)analysis to determine the population location of animal and human plague-infected strains in 2019,understand the relationship between the polymorphism and phylogeny of Y.pestis in different endemic counties or regions in Inner Mongolia,and use deeper differences in SNP Accurately distinguish and carry out traceability of human strains.Results All strains isolated from the Plague foci of the Inner Mongolia Autonomous Region in 2018 and 2019 are grouped into 2.MED3 lineages in phylogenetic tree,and these strains can be further divided into the four clades in 2.MED3 lineages.The 3 cases of 4 plague patients A/B,C,and D that occurred in 2019 were located in Clade II,I,and III respectively.2.MED3 lineages persisted in host animals,and caused different epidemic events in different regions and years in Inner Mongolia.Conclusion The phylogenetic relationship of the genome-wide SNPs shows that some strains isolated in 2018 from the Plague foci of the Inner Mongolia Autonomous Region and the 2019 strain show homologous phylogenetic characteristics.In 2019,there was more rainfall and good grass growth,which greatly increased the number of rodents,especially the main host,Mongolian gerbils,and made the plague in the gerbils foci again violently active.The rodent density of the gerbil plague foci in the Inner Mongolia Plateau shows a trend of increasing first and then decreasing,which is a prerequisite for the occurrence of the plague.In epidemiological investigations,the use of reliable subtype methods is a prerequisite for identifying connections between isolates and understanding the dynamics of pathogen transmission.When the culture of clinical specimens fails or the sequence of these pathogens is not enough to establish a phylogenetic tree through SNPs,PCR-based molecular methods such as MLVA or typical SNP analysis can be used to establish it.It is the best choice to use whole-genome SNP for traceability analysis during an outbreak.