Strategy for Sensitive and Specific Detection of Yersinia pestis in Skeletons of the Black Death Pandemic
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{"title"=>"Strategy for Sensitive and Specific Detection of Yersinia pestis in Skeletons of the Black Death Pandemic", "type"=>"journal", "authors"=>[{"first_name"=>"Lisa", "last_name"=>"Seifert", "scopus_author_id"=>"55754977200"}, {"first_name"=>"Michaela", "last_name"=>"Harbeck", "scopus_author_id"=>"6602787426"}, {"first_name"=>"Astrid", "last_name"=>"Thomas", "scopus_author_id"=>"35390067300"}, {"first_name"=>"Nadja", "last_name"=>"Hoke", "scopus_author_id"=>"52463664700"}, {"first_name"=>"Lothar", "last_name"=>"Zöller", "scopus_author_id"=>"7007064195"}, {"first_name"=>"Ingrid", "last_name"=>"Wiechmann", "scopus_author_id"=>"6602663653"}, {"first_name"=>"Gisela", "last_name"=>"Grupe", "scopus_author_id"=>"7003537958"}, {"first_name"=>"Holger C.", "last_name"=>"Scholz", "scopus_author_id"=>"7202371399"}, {"first_name"=>"Julia M.", "last_name"=>"Riehm", "scopus_author_id"=>"35488808200"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84884276688", "sgr"=>"84884276688", "pui"=>"369833853", "pmid"=>"24069445", "doi"=>"10.1371/journal.pone.0075742"}, "id"=>"b65dd281-9a4d-3887-827d-9075dcc17a36", "abstract"=>"Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14(th) century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study.", "link"=>"http://www.mendeley.com/research/strategy-sensitive-specific-detection-yersinia-pestis-skeletons-black-death-pandemic", "reader_count"=>34, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>2, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>2, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>2, "Arts and Humanities"=>2, "Design"=>1, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>3, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}}, "reader_count_by_country"=>{"United States"=>2, "Norway"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1206793"], "description"=>"<p>Schematic workflow for the proceeding through highly optimized and validated protocols for the detection of <i>Y. pestis</i> from ancient samples.</p>", "links"=>[], "tags"=>["workflow", "proceeding", "optimized", "validated", "protocols", "detection"], "article_id"=>801238, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Lisa Seifert", "Michaela Harbeck", "Astrid Thomas", "Nadja Hoke", "Lothar Zöller", "Ingrid Wiechmann", "Gisela Grupe", "Holger C. Scholz", "Julia M. Riehm"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0075742.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_workflow_for_the_proceeding_through_highly_optimized_and_validated_protocols_for_the_detection_of_Y_pestis_from_ancient_samples_/801238", "title"=>"Schematic workflow for the proceeding through highly optimized and validated protocols for the detection of <i>Y. pestis</i> from ancient samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-17 01:38:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1206795"], "description"=>"<p>The profile represents a typical collagenous pattern with a high amino acid yield. However, aspartic and glutamic acid concentrations are significantly reduced. At 72 min an unidentified peak was detected that did not show up in the other samples. </p>", "links"=>[], "tags"=>["specimen", "mp"], "article_id"=>801240, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Lisa Seifert", "Michaela Harbeck", "Astrid Thomas", "Nadja Hoke", "Lothar Zöller", "Ingrid Wiechmann", "Gisela Grupe", "Holger C. Scholz", "Julia M. Riehm"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0075742.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acid_profile_of_specimen_MP_59_I_channel_1_570_nm_and_2_440_nm_/801240", "title"=>"Amino acid profile of specimen MP 59-I, channel 1 (570 nm) and 2 (440 nm).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-17 01:38:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1206797"], "description"=>"<div><p>A) Amplification products of the synthetic <i>pla</i> construct at concentrations of 10, 5 and 1 copy, respectively, are shown. Three samples were extracted from ancient bones originating from a modern time cemetery lacking any <i>Y. pestis</i> specific amplicons (bone matrix).</p>\n\t\t\t\t\t\t<p>B) Besides the synthetic <i>pla</i> construct, the gel shows products of PCR reactions set up, containing 1 ng DNA of each from the negative panel organisms (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075742#pone-0075742-t002\" target=\"_blank\">Table 2</a>).</p>\n\t\t\t\t\t\t<p>C) Gel showing amplification products of aDNA extracted from teeth (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075742#pone-0075742-t001\" target=\"_blank\">Table 1</a>). M: marker, PC: positive control, NTC: no template control, MMC: master mix control, WC: water control, MP: Manching-Pichl, Germany, origin of individuals, E1-8: extraction controls, Ba: Basel, Switzerland, origin of individuals, B: Brandenburg, Germany, origin of individuals.</p></div>", "links"=>[], "tags"=>["pcr", "targeting", "133", "bp"], "article_id"=>801242, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Lisa Seifert", "Michaela Harbeck", "Astrid Thomas", "Nadja Hoke", "Lothar Zöller", "Ingrid Wiechmann", "Gisela Grupe", "Holger C. Scholz", "Julia M. Riehm"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0075742.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conventional_PCR_targeting_a_133_bp_fragment_of_Y_pestis_pla_gene_/801242", "title"=>"Conventional PCR targeting a 133 bp fragment of <i>Y. pestis pla</i> gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-17 01:38:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1206799"], "description"=>"<p>qPCR targeting <i>Y. pestis pla</i> gene screening ancient samples.</p>", "links"=>[], "tags"=>["targeting"], "article_id"=>801244, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Lisa Seifert", "Michaela Harbeck", "Astrid Thomas", "Nadja Hoke", "Lothar Zöller", "Ingrid Wiechmann", "Gisela Grupe", "Holger C. Scholz", "Julia M. Riehm"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0075742.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_qPCR_targeting_Y_pestis_pla_gene_screening_ancient_samples_/801244", "title"=>"qPCR targeting <i>Y. pestis pla</i> gene screening ancient samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-17 01:38:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1206804", "https://ndownloader.figshare.com/files/1206805", "https://ndownloader.figshare.com/files/1206806"], "description"=>"<div><p><i>Yersinia pestis</i> has been identified as the causative agent of the Black Death pandemic in the 14<sup>th</sup> century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the <i>Y. pestis</i> specific <i>pla</i> gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both <i>Y. pestis</i> specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 <i>Y. pseudotuberculosis</i> strains as well as for DNA of 22 <i>Y. pestis</i> strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study.</p> </div>", "links"=>[], "tags"=>["detection", "skeletons", "pandemic"], "article_id"=>801249, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Lisa Seifert", "Michaela Harbeck", "Astrid Thomas", "Nadja Hoke", "Lothar Zöller", "Ingrid Wiechmann", "Gisela Grupe", "Holger C. Scholz", "Julia M. Riehm"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0075742.s001", "https://dx.doi.org/10.1371/journal.pone.0075742.s002", "https://dx.doi.org/10.1371/journal.pone.0075742.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Strategy_for_Sensitive_and_Specific_Detection_of_Yersinia_pestis_in_Skeletons_of_the_Black_Death_Pandemic/801249", "title"=>"Strategy for Sensitive and Specific Detection of <i>Yersinia pestis</i> in Skeletons of the Black Death Pandemic", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-09-17 01:38:27"}

PMC Usage Stats | Further Information

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Relative Metric

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