Attenuation of virulence in Yersinia pestis across three plague pandemics.

Yersinia pestis has spilled over from wild rodent reservoirs to commensal rodents and humans, causing three historically recorded pandemics. Depletion in the copy number of the plasmid-encoded virulence gene pla occurred in later-dated strains of the first and second pandemics, yet the biological relevance of the pla deletion has been difficult to test. We identified modern Y. pestis strains that independently acquired the same pla depletion as ancient strains and herein show that excision of pla from the multicopy pPCP1 plasmid is accompanied by the integration of a separate full pPCP1 harboring pla into the single-copy pCD1 plasmid, reducing pla dosage. Moreover, we demonstrate that this depletion decreases the mortality of mice in models of bubonic plague but not in the pneumonic and septicemic forms of the disease. We hypothesize that pla depletion may have been selectively advantageous in bubonic plague, owing to rodent fragmentation after pandemic-induced mortality. Editor's summary: Plague has devastated human and rodent populations alike many times throughout history. Sidhu et al. tracked the genetics of virulence in the plague pathogen Yersinia pestis in ancient and modern samples. They observed that the bacterial virulence factor pla, a gene encoding a protease, periodically becomes depleted late in epidemics. The authors verified that pla depletion reduces virulence in mouse models of bubonic plague. Therefore, in response to high disease mortality, selection could act to attenuate virulence. This would allow the pathogen to persist in tolerant reservoir hosts when susceptible host populations fragment and pathogen transmission becomes uncertain. —Caroline Ash INTRODUCTION: The Plague of Justinian and the Black Death represent two of the greatest mortality events in recorded human history and are herald waves of the first and second plague pandemics. Genomes of the plague bacterium Yersinia pestis, reconstructed from ancient human remains from about a century into each pandemic, show evidence of a depletion in the copy number of the virulence gene pla, which resides on the high–copy number plasmid (pPCP1) and encodes a plasminogen activator (Pla) protease that is responsible for virulence and pathogenicity in bubonic and pneumonic models of plague. RATIONALE: To determine the effects of the pla depletion on virulence in mice, we tested modern (third pandemic) strains of Y. pestis from Vietnam that contain the same depletion as ancient strains using models of bubonic, pneumonic, and septicemic plague. We also investigated the genomes of the ancient and modern Y. pestis strains to characterize the molecular basis of the pla depletion. RESULTS: De novo reconstruction of the ancient and modern strains of Y. pestis that contain lower–copy number pla show transfer from the high–copy number plasmid (pPCP1) to single-copy genomic features in the modern (pCD1) and ancient (chromosome) strains. A common pla deletion mechanism is likely mediated by xrs sites present in pPCP1. Depletion in pla copy number led to an attenuation of virulence in bubonic models of plague (but not pneumonic or septicemic models), with lowered overall mortality (100 to 85%) and a longer time to death (by ~2 days). CONCLUSION: We hypothesize that natural selection for pla-reduced strains reflects the metapopulation structure of rat populations, supporting epidemiological models in which pathogen attenuation enables disease persistence in small and fragmented populations through frequent, reinitiated epidemics after population recovery. The massive rat mortality that presumably occurred during the first and second pandemics likely led to suppressed rodent densities. By increasing population fragmentation, this created an environment that favored pla-reduced, attenuated strains of Y. pestis over their more virulent wild-type pla relatives. Specifically, a decreased mortality rate and longer time to host death would allow for the continued movement of rodents between existing populations, now more distantly spaced than early in the pandemic, allowing for the continued persistence, and hence increased transmission, of Y. pestis and the slow continual burn of the epidemic. Graphical representation of our working hypothesis.: Rodent metapopulation structure and size are critical selective pressures for virulence attenuation in the plague bacterium Y. pestis. The Black Death and subsequent epidemics of the second pandemic continually suppressed population sizes of key amplifying hosts (black rats), eventually reaching a threshold at which depletion in the virulence gene pla swept across most European strains. Depletion of the pla gene lowers overall mortality in bubonic models of plague and increases the time to death, allowing for the more sparsely populated rats to reach new hosts that are now more distantly spaced. [Figure created with BioRender.com] [ABSTRACT FROM AUTHOR]