Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck

Abstract

Medieval Europe was repeatedly affected by outbreaks of infectious diseases, some of which reached epidemic proportions. A Late Medieval mass burial next to the Heiligen-Geist-Hospital in Lübeck (present-day Germany) contained the skeletal remains of more than 800 individuals who had presumably died from infectious disease. From 92 individuals, we screened the ancient DNA extracts for the presence of pathogens to determine the cause of death. Metagenomic analysis revealed evidence of Salmonella enterica subsp. enterica serovar Paratyphi C, suggesting an outbreak of enteric paratyphoid fever. Three reconstructed S. Paratyphi C genomes showed close similarity to a strain from Norway (1200 CE). Radiocarbon dates placed the disease outbreak in Lübeck between 1270 and 1400 cal CE, with historical records indicating 1367 CE as the most probable year. The deceased were of northern and eastern European descent, confirming Lübeck as an important trading center of the Hanseatic League in the Baltic region.

Keywords: Microbiology; Paleontology.

Graphical abstract

Figure 1

The excavation site of the Heiligen-Geist-Hospital (HGH) in Lübeck (A) Location of Lübeck in present-day northern Germany. (B–D) (B) Plan of the HGH building complex. The mass graves 4528 and 4529 and the two multiple burial pits 4562 and 4571 are indicated. All S. Paratyphi C-positives were found in the pits 4562 (C) and 4571 (D).

Figure 2

Phylogenetic relationship of ancient and modern Salmonella enterica genomes Bayesian phylogenetic tree of three genomes from the HGH mass burial site in Lübeck (red), nine ancient (blue), and 123 modern (black) S. enterica genomes. S. enterica subsp. arizonae RKS2983 is used as out-group. Branches of the same serovars are collapsed, and the number of combined reference genomes is given in brackets. Nodes are labeled with posterior probabilities estimated by MrBayes. Branch lengths correspond to the number of substitutions per site. An enlarged section of the three HGH Lübeck genomes as well as those from Ragna and Tepos is provided in Figure S4.

Figure 3

Population genetic analysis Principal component analysis (PCA) of HGH individuals (red circles) from Lübeck in the context of 19 modern-day European populations. A PCA with a larger set of reference populations is shown in Figure S5.