Investigating the genetic and biological mechanisms governing pathogenic Yersinia species survival in soil and plague re-emergence
Publication Date
July 27, 2026
Abstract
Yersinia pestis is the causative agent of human plague and evolved from its ancestor Yersinia pseudotuberculosis, an enteropathogen approximately 1,500-20,000 years ago. Y. pestis and Y. pseudotuberculosis share 98% genomic identity, suggesting that small genetic changes have driven Y. pestis’ evolution and distinction in disease phenotype from its predecessor. Plague is transmitted between rodents and humans via a flea vector. However, aspects of the lifestyle of Y. pestis are not well understood.
Plague characteristically disappears from plague foci for decades between outbreaks and is not recovered from rodent or flea hosts. This questions where the pathogen is located, how it is surviving during interepizootic periods, and how it re-emerges in plague foci. Based on genetic homology, Y. pseudotuberculosis and Y. pestis may share additional unidentified characteristics. As Y. pseudotuberculosis is a soil-borne pathogen, Y. pestis may also survive in soil during interepizootic periods, providing an explanation to how plague re-emerges in plague foci. Preliminary work has found that Y. pestis can survive in soil, however, the ability for Y. pestis to survive long-term in natural soils and the mechanisms of how Y. pestis and Y. pseudotuberculosis survive in soil has not been studied.
This project aims to investigate the genetic and/ or biological mechanisms that drive Y. pseudotuberculosis and Y. pestis to survive in natural soils. This study found that parent Y. pseudotuberculosis and Y. pestis strains (YPIII and CO92 respectively) can be cultivated from sterile (gamma-irradiated) soils after at least 168 days and 112 days post-inoculation (dpi) respectively and retain the virulence plasmid (pYV in Y. pseudotuberculosis and pCD1 in Y. pestis). In non-sterile soils, parent YPIII and CO92 strains can be cultivated after at least 28 dpi while retaining the virulence plasmid. Testing gene knockout mutant strains found that the YPIII dI (ΔypsI/ ΔytbI) strain which lacks acyl homoserine lactone synthases has a significant reduction in recovery from non-sterile soil compared to the parent strain, highlighting the importance of quorum sensing, in particular acyl homoserine lactone synthesis in the presence of the soil microbiota.
RNA-seq studies found that RNA could be successfully extracted from soil and that differential gene expression occurs in Y. pseudotuberculosis and Y. pestis in soil in comparison to Yersinia Defined Minimal Media. Further RNA-seq experiments highlighted that Y. pseudotuberculosis and Y. pestis display differential gene expression in soil in a time-dependent manner where specific gene sets were only upregulated in soil after 7- and 28-dpi. Over-representation analysis (ORA) of upregulated genes in soil found that ATP-binding cassette (ABC) transporters were significantly overrepresented for both YPIII and CO92 and Quorum Sensing systems were overrepresented in YPIII.
Transposon Directed Insertion-site Sequencing (TraDIS) was used to determine the essential genome of YPIII and identified 386 protein coding genes that could not be mutated in the generated library. Screening of this TraDIS library found that genes involved in the biosynthesis of the lipopolysaccharide (LPS) were important for survival in sterile and non-sterile model soil but not in Yersinia Defined Minimal Media.
Overall, this study has provided further evidence that Y. pseudotuberculosis and Y. pestis can survive in natural soils and retain the virulence plasmid to potentially initiate a new disease outbreak. This work suggests that some systems such as ABC transporters and the LPS are important in both Y. pseudotuberculosis and Y. pestis to survive in soil. This study also emphasized how the soil microbiota can influence the genetic factors that permit survival of pathogenic Yersinia species in the environment.
Future work from this study would include performing survival assays from soil collected from plague endemic and non-endemic sites of Madagascar; an existing plague focus to observe if Y. pestis can survive longer in non-sterile soil from plague endemic regions as a potential strategy of interepizootic persistence. Other studies would involve generating a high density TraDIS library in Y. pestis to determine which genes are important for survival in soil and to compare the results obtained in this study to see if Y. pestis and Y. pseudotuberculosis share genes to permit survival in the environment. Furthermore, additional studies to compare genes needed for Y. pestis to switch from survival in soil to host infection is of vital importance to understand how plague re-emerges in plague foci.
Item Type
ethesis
Thesis Type
PhD
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secondary supervisor
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