Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
Identifieur interne : 000080 ( Pmc/Checkpoint ); précédent : 000079; suivant : 000081Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
Auteurs : Gemma L. Kay ; Martin J. Sergeant ; Valentina Giuffra ; Pasquale Bandiera ; Marco Milanese ; Barbara Bramanti ; Raffaella Bianucci ; Mark J. PallenSource :
- mBio [ 2150-7511 ] ; 2014.
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
Url:
DOI: 10.1128/mBio.01337-14
PubMed: 25028426
PubMed Central: 4161259
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Recovery of a Medieval <italic>Brucella melitensis</italic> Genome Using Shotgun Metagenomics</title><author><name sortKey="Kay, Gemma L" sort="Kay, Gemma L" uniqKey="Kay G" first="Gemma L." last="Kay">Gemma L. Kay</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sergeant, Martin J" sort="Sergeant, Martin J" uniqKey="Sergeant M" first="Martin J." last="Sergeant">Martin J. Sergeant</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Giuffra, Valentina" sort="Giuffra, Valentina" uniqKey="Giuffra V" first="Valentina" last="Giuffra">Valentina Giuffra</name></author><author><name sortKey="Bandiera, Pasquale" sort="Bandiera, Pasquale" uniqKey="Bandiera P" first="Pasquale" last="Bandiera">Pasquale Bandiera</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Milanese, Marco" sort="Milanese, Marco" uniqKey="Milanese M" first="Marco" last="Milanese">Marco Milanese</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Bramanti, Barbara" sort="Bramanti, Barbara" uniqKey="Bramanti B" first="Barbara" last="Bramanti">Barbara Bramanti</name><affiliation><nlm:aff id="aff5"></nlm:aff></affiliation></author><author><name sortKey="Bianucci, Raffaella" sort="Bianucci, Raffaella" uniqKey="Bianucci R" first="Raffaella" last="Bianucci">Raffaella Bianucci</name></author><author><name sortKey="Pallen, Mark J" sort="Pallen, Mark J" uniqKey="Pallen M" first="Mark J." last="Pallen">Mark J. Pallen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25028426</idno><idno type="pmc">4161259</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161259</idno><idno type="RBID">PMC:4161259</idno><idno type="doi">10.1128/mBio.01337-14</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000400</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000400</idno><idno type="wicri:Area/Pmc/Curation">000400</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000400</idno><idno type="wicri:Area/Pmc/Checkpoint">000080</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000080</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Recovery of a Medieval <italic>Brucella melitensis</italic> Genome Using Shotgun Metagenomics</title><author><name sortKey="Kay, Gemma L" sort="Kay, Gemma L" uniqKey="Kay G" first="Gemma L." last="Kay">Gemma L. Kay</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Sergeant, Martin J" sort="Sergeant, Martin J" uniqKey="Sergeant M" first="Martin J." last="Sergeant">Martin J. Sergeant</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Giuffra, Valentina" sort="Giuffra, Valentina" uniqKey="Giuffra V" first="Valentina" last="Giuffra">Valentina Giuffra</name></author><author><name sortKey="Bandiera, Pasquale" sort="Bandiera, Pasquale" uniqKey="Bandiera P" first="Pasquale" last="Bandiera">Pasquale Bandiera</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Milanese, Marco" sort="Milanese, Marco" uniqKey="Milanese M" first="Marco" last="Milanese">Marco Milanese</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Bramanti, Barbara" sort="Bramanti, Barbara" uniqKey="Bramanti B" first="Barbara" last="Bramanti">Barbara Bramanti</name><affiliation><nlm:aff id="aff5"></nlm:aff></affiliation></author><author><name sortKey="Bianucci, Raffaella" sort="Bianucci, Raffaella" uniqKey="Bianucci R" first="Raffaella" last="Bianucci">Raffaella Bianucci</name></author><author><name sortKey="Pallen, Mark J" sort="Pallen, Mark J" uniqKey="Pallen M" first="Mark J." last="Pallen">Mark J. Pallen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>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 <italic>Brucella melitensis</italic> 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 <italic>B. melitensis</italic> strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS<italic>711</italic> insertions. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">mBio</journal-id><journal-id journal-id-type="iso-abbrev">MBio</journal-id><journal-id journal-id-type="hwp">mbio</journal-id><journal-id journal-id-type="pmc">mbio</journal-id><journal-id journal-id-type="publisher-id">mBio</journal-id><journal-title-group><journal-title>mBio</journal-title></journal-title-group><issn pub-type="epub">2150-7511</issn><publisher><publisher-name>American Society of Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25028426</article-id><article-id pub-id-type="pmc">4161259</article-id><article-id pub-id-type="publisher-id">mBio01337-14</article-id><article-id pub-id-type="doi">10.1128/mBio.01337-14</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Recovery of a Medieval <italic>Brucella melitensis</italic> Genome Using Shotgun Metagenomics</article-title><alt-title>Medieval <italic>Brucella melitensis</italic> Genome</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kay</surname><given-names>Gemma L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sergeant</surname><given-names>Martin J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Giuffra</surname><given-names>Valentina</given-names></name><xref ref-type="aff" rid="aff2 aff3"><sup>b,c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bandiera</surname><given-names>Pasquale</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Milanese</surname><given-names>Marco</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bramanti</surname><given-names>Barbara</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Bianucci</surname><given-names>Raffaella</given-names></name><xref ref-type="aff" rid="aff5 aff6 aff7"><sup>e,f,g</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Pallen</surname><given-names>Mark J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><aff id="aff1"><label><sup>a</sup></label>Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom</aff><aff id="aff2"><label><sup>b</sup></label>Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy</aff><aff id="aff3"><label><sup>c</sup></label>Department of Biomedical Sciences, Human Anatomy, University of Sassari, Sassari, Italy</aff><aff id="aff4"><label><sup>d</sup></label>Department of History, University of Sassari, Sassari, Italy</aff><aff id="aff5"><label><sup>e</sup></label>Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway</aff><aff id="aff6"><label><sup>f</sup></label>Department of Public Health and Pediatric Sciences, Laboratory of Physical Anthropology, University of Turin, Turin, Italy.</aff><aff id="aff7"><label><sup>g</sup></label>Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Université, Marseille, France</aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Raffaella Bianucci, <email>raffaella.bianucci@unito.it</email>, or Mark J. Pallen, <email>m.pallen@warwick.ac.uk</email>.</corresp><fn fn-type="equal"><p>G.L.K. and M.J.S. and R.B. and M.J.P. contributed equally to this work.</p></fn><fn fn-type="edited-by"><p><bold>Editor</bold> Paul Keim, Northern Arizona University</p></fn></author-notes><pub-date pub-type="epub"><day>15</day><month>7</month><year>2014</year></pub-date><pub-date pub-type="collection"><season>Jul-Aug</season><year>2014</year></pub-date><volume>5</volume><issue>4</issue><elocation-id>e01337-14</elocation-id><history><date date-type="received"><day>15</day><month>5</month><year>2014</year></date><date date-type="accepted"><day>11</day><month>6</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Kay et al.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Kay et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license</ext-link>, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><title>ABSTRACT</title><p>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 <italic>Brucella melitensis</italic> 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 <italic>B. melitensis</italic> strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS<italic>711</italic> insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens.</p></abstract><abstract abstract-type="executive-summary"><title>IMPORTANCE</title><p>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 <italic>Brucella melitensis</italic> 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.</p></abstract><counts><page-count count="6"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>July/August 2014</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Bandiera, Pasquale" sort="Bandiera, Pasquale" uniqKey="Bandiera P" first="Pasquale" last="Bandiera">Pasquale Bandiera</name><name sortKey="Bianucci, Raffaella" sort="Bianucci, Raffaella" uniqKey="Bianucci R" first="Raffaella" last="Bianucci">Raffaella Bianucci</name><name sortKey="Bramanti, Barbara" sort="Bramanti, Barbara" uniqKey="Bramanti B" first="Barbara" last="Bramanti">Barbara Bramanti</name><name sortKey="Giuffra, Valentina" sort="Giuffra, Valentina" uniqKey="Giuffra V" first="Valentina" last="Giuffra">Valentina Giuffra</name><name sortKey="Kay, Gemma L" sort="Kay, Gemma L" uniqKey="Kay G" first="Gemma L." last="Kay">Gemma L. Kay</name><name sortKey="Milanese, Marco" sort="Milanese, Marco" uniqKey="Milanese M" first="Marco" last="Milanese">Marco Milanese</name><name sortKey="Pallen, Mark J" sort="Pallen, Mark J" uniqKey="Pallen M" first="Mark J." last="Pallen">Mark J. Pallen</name><name sortKey="Sergeant, Martin J" sort="Sergeant, Martin J" uniqKey="Sergeant M" first="Martin J." last="Sergeant">Martin J. Sergeant</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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