Metagenomic analysis of skeletons found at a Late Medieval-age mass burial site in Lübeck, Germany, provides evidence of an enteric paratyphoid fever outbreak in the area but no evidence of the bubonic plague, contradicting expectations of archaeologists and anthropologists.

Examining ancient DNA from the teeth and bones of 92 individuals from the Lübeck mass burial site, the researchers found evidence in eight individuals of infection with the bacterium Salmonella enterica — in particular, the subspecies of this pathogen known as serovar Paratyphoid C, or S. Paratyphoid C. This evidence suggests an outbreak of an enteric paratyphoid fever that spread through the city of Lübeck in the late 14th century, a fever that still affects about 5 million people per year and kills approximately 54,000, according to the researchers. 

The mass burial site is formed by two mass graves and two smaller pits. It was found in 1989 next to the Heiligen-Geist Hospital in Lübeck, originally a monastery that was converted to a hospital in 1226 CE, according to Ben Krause-Kyora, professor at Kiel University and lead author of the study, published April 13 in iScience.

The mass burial site contained the remains of more than 800 individuals from the Late Middle Ages, and the lack of traumatic lesions on the bones indicated that these may be victims of an epidemic event, according to the researchers.

Archaeologists and anthropologists guessed that the most likely epidemic event that killed the victims was the bubonic plague, since Lübeck was known to have had several outbreaks, first in 1350 and again in 1359. Radiocarbon dating places the mass burial sites in the time range of 1270 to 1400 — roughly the same time that the Black Death spread across Europe. 

However, no sign of Yersinia pestis, which caused the Black Death, was found in individuals or in samples from the mass burial site. 

Present-day Lübeck is a "really nicely preserved medieval town," Krause-Kyora said, and in medieval times, it was a densely populated melting pot of diverse people. It attracted merchants, sailors and workers from all around the Baltic region. 

In line with Lübeck's importance as a medieval trading center, the genetic analysis of the victims showed that the dead represented a varied group of people of northern and eastern European descent. 

"Back then it was one of the major trading hubs, more or less, in northern Europe," Krause-Kyora said. "So, it connected the Baltic Sea with the North Sea, and everything which was distributed in the Baltics was distributed via Lübeck, more or less."

By the standards of the time, Lübeck was a clean city, according to the researchers, and so it was a surprise to find evidence of a paratyphoid fever outbreak in the area.

S. Paratyphoid C bacteria grow in the intestines and blood, and quickly spread through food and water contaminated with the feces of infected individuals. The transmission of the bacteria often occurs when individuals do not wash their hands before preparing or handling food, according to the researchers. 

Though the researchers are not able to conclude where this pathogen emanated from or how it spread, three reconstructed S. Paratyphoid C genomes showed close similarity to a strain from Norway dated to roughly around 1200. 

This pathogen is "more or less today extinct from Central Europe, because of better hygiene," Krause-Kyora said, "but it's still present in really remote areas of the world … nowadays a minority of infected cases."

From an archaeological perspective, this research functions as a "proof of principle" that metagenomic analysis can identify a historical epidemic caused by a bacterium or virus, allowing this type of research to contribute to medieval history and to help define epidemic outbreaks, according to Krause-Kyora. 

"This is really an outlook for future studies," he said. "This was the first task — to identify the pathogen. Now we can address more questions about immune genes, for example, and see how these epidemics really have shaped us."

The study "Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck," published April 13 in iScience, was co-authored by Ben Krause-Kyora, Gerhard Fouquet, Magdalena Haller, Julian Susat, Alexander Immel, Andre Franke and Almut Nebel, Kiel University; Anna Lena Flux and Susanne Hummel, University of Göttingen; Alexander Herbig and Johannes Krause, Max Planck Institute for the Science of Human History; Kimberly Callan, Kiel University and Harvard Medical School; Anne Kupczok, Kiel University and Wageningen University & Research; and Dirk Rieger, Hanseatic City of Lübeck Historical Monuments Protection Authority.