Salmonella enterica genomes from victims of a major 16th century epidemic in Mexico. TeposParaC

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Introducing a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic, which affected large parts of Mexico. Locally this epidemic was known as “cocoliztli”, the pathogenic cause of which has been debated for over a century. Here we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.

美洲原住民群体在欧洲早期接触时期因传染病遭遇极高死亡率，其中多数传染病由欧洲殖民者引入。引发这些疫情的致病病原体大多仍未被探明。本研究引入一款名为MALT的宏基因组分析工具，用于搜寻古代病原体DNA痕迹，最终在墨西哥南部瓦哈卡州Teposcolula-Yucundaa的一处早期接触时代疫病墓葬群的个体遗骸中，成功检出肠炎沙门氏菌（Salmonella enterica）。结合历史与考古证据，该墓葬群可确认与公元1545-1550年波及墨西哥大片区域的疫情相关，当地将这场疫情称为“cocoliztli”，其致病病因已争论逾百年。本研究报道了10份肠炎沙门氏菌肠炎亚种（Salmonella enterica subsp. enterica）副伤寒C血清型的全基因组数据，该细菌是引发肠热症的致病菌之一。我们提出，副伤寒C沙门氏菌（S. Paratyphi C）可作为Teposcolula-Yucundaa地区1545年cocoliztli疫情导致人口锐减的强力候选致病原。