Salmonella entericagenomes recovered from victims of a major 16th century epidemic in Mexico

Abstract

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. Using a metagenomic tool called MALT 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 to the 1545-1550 CE epidemic locally known as "cocoliztli", the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico.One Sentence Summary: Genomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.

Millennia of Genomic Stability within the Invasive Para C Lineage of <i>Salmonella enterica</i>

“…In turn, the estimated tMRCA for Paratyphi C, Typhisuis plus Choleraesuis was 3,943 y, and that ancestor evolved in Europe according to three independent Bayesian and maximum-likelihood methods (figure S8, table S14). We note that a European ancestry is consistent with the existence of Ragna in northern Norway 800 years ago, and of other Paratyphi C genomes in Mexico in 1,545 CE that may have been imported to the New World by Europeans (32). We also note that serovars Choleraesuis and Typhisuis infect swine, and that the tMRCA dates overlap with the Neolithic domestication of pigs from wild boar in Europe (33) (Fig.…”

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“…In the period of Asif ud Daula, another royal lady besides Sadar un Nisa emerged as a powerful figure in the court. She was Bahu Begum (Aliya Begum), mother of Asif ud Daula, sister of Najam ud Daula, 25 daughter of Motam ud Daula (governor of Gujrat) and foster child of King Muhammad Shah. She was Chief wife of Shuja ud Daula and was given high respect and esteem by royal family of Awadh due to her respectable lineage.…”

“…Since the original works of the late '90s, 23 examinations of series supposedly linked to plague have multiplied and the expansion in paleogenomics has driven spectacular advances in knowledge of the evolutionary history of the Yersinia pestis bacterium during its different pandemics. 24 Other studies have allowed recognizing additional pathogens such as Salmonella enterica, responsible for typhoid fever 25 or Rickettsia prowazekii, accountable for typhus. 26 By permitting the identification of these pathogens, paleomicrobiology, a research field in constant progression, has enabled archaeology to transcend some of the limitations it traditionally faced.…”

“…The recent thesis of Théodossios Polychronis is a witness to that. In a monumental work of reinterpreting and retranslating the fragments of Hellanicus, 25 25. Polychronis' thesis offered a solid study of Hellanicus' production and the main questions of the beginnings of historiography in Greece itself.…”

The efficacy of whole human genome capture on ancient dental calculus and dentin

“…Sequence capture additionally reduces the amount of material required for destructive analyses, and decreases the experimental workload and cost of aDNA analysis (Ávila‐Arcos et al, ; Carpenter et al, ). To date, targeted enrichment of archaeological specimens has resulted in the successful retrieval of ancient mitochondrial genomes (e.g., Briggs et al, ; Llamas et al, ; Ozga et al, ; Slon et al, ), ancient pathogen genomes (Bos et al, ; Spyrou et al, ; Vågene et al, ), human genome‐wide SNPs (Haak et al, ), partial or whole exomes (Burbano et al, ; Da Fonseca et al, ), entire chromosomes (Cruz‐Dávalos et al, ; Fu, Meyer, et al, ), and partial nuclear genomes (Carpenter et al, ; Schroeder et al, ).…”