AncientClostridiumDNA and variants of tetanus neurotoxins associated with human archaeological remains

Abstract

SUMMARYThe analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, through a large-scale metagenomic analysis of archeological samples, we discovered bacterial species related to modern-dayClostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. We assembled draft genomes from 38 distinct human archeological samples spanning five continents and dating to as early as ~4000 BCE. These genomes had varying levels of completeness and a subset of them displayed hallmarks of ancient DNA damage. While 24 fall into knownC. tetaniclades, phylogenetic analysis revealed novelC. tetanilineages, as well as two novelClostridiumspecies (“Clostridiumsp. X and Y”) closely related toC. tetani. Within these genomes, we found 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from a ~6000-year-old Chilean mummy sample and found that it induced tetanus muscle paralysis in mice with potency comparable to modern TeNT. Our work identifies neurotoxigenicC. tetaniin ancient DNA, newClostridiumspecies unique to ancient human samples, and a novel variant of TeNT that can cause disease in mammals.