Ancient DNA implicates Salmonella Paratyphi C as a candidate pathogen in a thirteenth-century East Asian epidemic

Abstract

We screened ancient metagenomic data from 15 individuals from a mortuary context archaeologically dated to the 13th century at the Xiyang site (Shanxi, North China). Authentic Salmonella enterica subsp. enterica serovar Paratyphi C (SPC) reads were detected in 5/15 individuals, of which three met the damage-pattern and coverage criteria for downstream analyses. Ancient authenticity was supported by terminal deamination signatures, short fragment-length distributions, mapping stringency, and negative controls. Human genomic profiles indicate affinities consistent with contemporaneous North China agricultural populations. Archaeological and genetic context shows that these 15 individuals derived from six multi-individual burials and that they share no biological kinship ties across burials, indicating multi-household exposure rather than a single-family cluster. Given DNA preservation and assay sensitivity, pathogen detections represent a conservative lower bound, and the true number of infections likely exceeded the five SPC-positive cases observed. Read alongside contemporaneous reports of severe febrile outbreaks (1213–1232 CE), these detections are temporally and contextually concordant with epidemic activity, supporting a working hypothesis that SPC contributed to disease episodes in this period without implying exclusive event-level causation. We outline archaeological context and textual sources as non-exclusive lines of evidence and emphasize limitations, including modest sample size (n = 15; positives = 5), uncertain within-tomb simultaneity, and incomplete chronological precision. These findings extend the documented temporal and geographic range of SPC to 13th-century North China and motivate targeted capture, direct dating of sampled individuals, and broader regional screening to evaluate scale, timing, and aetiological heterogeneity.