Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus.

Kirsten I Bos,Jennifer Klunk,Debi Poinar,Jason Sahl,G Brian Golding,Verena J Schuenemann,Nicholas Waglechner,Edward C Holmes,Mathieu Fourment,Stephen A Forrest,Alexander Herbig,Melanie Kuch,David M Wagner,Paul Keim,Johannes Krause,Hendrik N Poinar,Olivier Dutour

doi:10.7554/elife.12994

Abstract

The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.

Highlights

The bacterium Yersinia pestis is among the most virulent pathogens known to cause disease in humans
It is possible that once introduced to Europe around the time of the Black Death, Y. pestis persisted there for centuries, cycling in and between rodent and human populations and being introduced or reintroduced to various regions throughout Europe (Carmichael, 2014). Another possibility is that plague did not persist long-term in European rodent populations, but rather was continually reintroduced from rodent plague foci in Asia (Schmid et al, 2015). To address this key issue in Y. pestis evolution and epidemiology, we investigated plague-associated skeletal material from one of the last well-documented European epidemics, the Great Plague of Marseille (1720–1722), that occurred in the Provence region of France at the end of the second pandemic
Skeletal material used in this investigation was sampled from the Observance (OBS) collection housed in the osteoarcheological library of the Regional Department of Archaeology, French Ministry of Culture, medical faculty of Aix-Marseille Universite

Summary

Introduction

The bacterium Yersinia pestis is among the most virulent pathogens known to cause disease in humans. As the agent of plague it is an existing threat to public health as the cause of both emerging and re-emerging rodent-derived epidemics in many regions of the world (Duplantier et al, 2005; Vogler et al, 2011; Gage and Kosoy, 2005). This, and its confirmed involvement in three major historical pandemics, have made it the subject of intense study. The first pandemic, known as the Justinian Plague, occurred from the 6th through the 8th centuries; the second

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