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. 2014 Jul 15;5(4):e01337-14.
doi: 10.1128/mBio.01337-14.

Recovery of a Medieval Brucella Melitensis Genome Using Shotgun Metagenomics

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Free PMC article

Recovery of a Medieval Brucella Melitensis Genome Using Shotgun Metagenomics

Gemma L Kay et al. mBio. .
Free PMC article

Abstract

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. Importance: Infectious diseases have shaped human populations and societies throughout history. The recovery of pathogen DNA sequences from human remains provides an opportunity to identify and characterize the causes of individual and epidemic infections. By sequencing DNA extracted from medieval human remains through shotgun metagenomics, without target-specific capture or amplification, we have obtained a draft genome sequence of an ~700-year-old Brucella melitensis strain. Using a variety of bioinformatic approaches, we have shown that this historical strain is most closely related to recent strains isolated from Italy, confirming the continuity of this zoonotic infection, and even a specific lineage, in the Mediterranean region over the centuries.

Figures

FIG 1
FIG 1
(A) Calcific nodules excavated from the pelvic girdle of skeleton 2658. (B) Size distribution of reads from sample 2568. (i) All reads from the initial MiSeq run (~2 m). (ii) Reads from the second Miseq run (>20 m) which aligned with the B. melitensis 16 M genome. (iii) Reads from the dedicated run which mapped to the human genome (hg19). (C) Coverage plot of reads from sample 2568 mapped against the two chromosomes from the B. melitensis 16 M genome. The plot shows the average coverage and standard deviation for each 5,000-bp region in the genome. (D) Evidence of sequence damage associated with aged DNA showing the frequency of C-to-T and G-to-A transitions at the 5′ and 3′ ends of DNA fragments, respectively.
FIG 2
FIG 2
Phylogenetic tree showing the position of the medieval Geridu-1 strain within the Ether clade. Only those SNPs which correlated with sufficient coverage in the Geridu-1 alignment were included in the construction of the tree.

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