Kay, Gemma L. and Sergeant, Martin J. and Giuffra, Valentina and Bandiera, Pasquale and Milanese, Marco and Bramanti, Barbara and Bianucci, Raffealla and Pallen, Mark J. (2014) Recovery of a medieval Brucella melitensis genome using shotgun metagenomics. mBio, Vol. 5 (4), e01337-14. eISSN 2150-7511. Article.
Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens.
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