Antibiotic resistance is ancient

Journal name:
Nature
Volume:
477,
Pages:
457–461
Date published:
DOI:
doi:10.1038/nature10388
Received
Accepted
Published online

The discovery of antibiotics more than 70years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes1, 2. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics3. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to β-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.

At a glance

Figures

  1. Stratigraphic profile and location of Bear Creek site.
    Figure 1: Stratigraphic profile and location of Bear Creek site.

    Elevation is given in metres above base of exposure. Permafrost samples from below Dawson tephra were dated to about 30kyr bp. Preservation of the ice below and above the sample indicates that the sediments have not thawed since deposition. Silhouettes represent mammals and birds identified from ancient DNA sequences that are typical of the regional Late Pleistocene environment. aDNA, ancient DNA.

  2. Genetic diversity of ancient antibiotic resistance elements.
    Figure 2: Genetic diversity of ancient antibiotic resistance elements.

    a, b, Unrooted Bayesian phylogenies of translated β-lactamase (bla) (a) and tetracycline resistance (tetM) (b). Blue denotes predicted resistance enzymes, and green those associated with other functions; permafrost-derived sequences are labelled with the originating core name. Sequences in which resistance activity has been biochemically verified are noted with a single asterisk (Supplementary Information). The scale bar represents 0.1 substitutions per site. Posterior probabilities are shown for a, and those of 0.7 or more are indicated for b. All unlabelled tips derive from ancient sequences. BC1, Bear Creek sample 1; BC4, Bear Creek sample 4.

  3. Ancient vancomycin resistance elements.
    Figure 3: Ancient vancomycin resistance elements.

    a, vanHAX amplicons used in this study, with primer names noted above each arrow. b, Unrooted Bayesian phylogeny of translated vanA sequences; blue denotes strains with vanHAX clusters confirmed to confer resistance; sequences containing stop codons but homology throughout are noted with a single asterisk (Supplementary Information). BC1, Bear Creek sample 1; BC4, Bear Creek sample 4. c, VanAA2 structure. Left: ribbon diagram of the VanAA2 dimer (blue) overlaid with modern VanA (green), where the Ω-loop is coloured red; right: ball-and-stick representation of ATP binding. The electron density shown is an FoFc map contoured at 3σ. d, Comparison of modern and ancient VanA monomer structures. The Ω-loop is coloured red and detailed in the ball-and-stick figures. Ligands are shown in grey. Dashed lines represent hydrogen bonds.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

References

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Author information

  1. These authors contributed equally to this work.

    • Vanessa M. D’Costa &
    • Christine E. King

Affiliations

  1. Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5

    • Vanessa M. D’Costa,
    • Lindsay Kalan,
    • Mariya Morar,
    • Hendrik N. Poinar &
    • Gerard D. Wright
  2. Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5

    • Vanessa M. D’Costa,
    • Lindsay Kalan,
    • Mariya Morar &
    • Gerard D. Wright
  3. McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada, L8S 4L9

    • Christine E. King,
    • Carsten Schwarz &
    • Hendrik N. Poinar
  4. Department of Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4K1

    • Christine E. King,
    • Wilson W. L. Sung,
    • G. Brian Golding &
    • Hendrik N. Poinar
  5. Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E3

    • Duane Froese &
    • Fabrice Calmels
  6. Yukon Palaeontology Program, Department of Tourism and Culture, Yukon Government, PO Box 2703, Whitehorse, Yukon, Canada, Y1A 2C6

    • Grant Zazula
  7. Muséum National d’Histoire Naturelle, UMR 7206 Eco-anthropologie, 57rue Cuvier, CP139, 75231 Paris cedex 05, France

    • Regis Debruyne

Contributions

D.F., G.Z. and F.C. collected permafrost cores and performed geochemical analyses followed by subsampling by C.S., V.M.D. and C.E.K. C.E.K performed ancient DNA laboratory work and 454 sequencing. V.M.D. designed primers for resistance genes, 16S and gfp. V.M.D. and C.E.K. designed and optimized the qPCR assays, and cloned and sequenced the resistance gene products. R.D. independently confirmed the results in France. L.K. purified and characterized VanA, and M.M. crystallized VanA and determined the three-dimensional structure. W.S., G.B.G., C.E.K. and H.N.P. processed and analysed the floral/faunal data; V.M.D. and G.B.G. performed phylogenetic and bioinformatic analyses of the resistance gene sequences. H.N.P. and G.D.W. conceived the project, and V.M.D., C.E.K., D.F., H.N.P. and G.D.W. wrote the manuscript. All authors edited the final draft.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

The metagenomic sequences determined from permafrost are deposited in GenBank under accession numbers JN316287–JN366376.

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Supplementary information

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  1. Supplementary Information (3M)

    The file contains Supplementary Text, Supplementary Figures 1-14 with legends and Supplementary Tables 1-12.

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