When are pathogen genome sequences informative of transmission events?
Publication Date
February 08, 2018
Authors
Finlay Campbell, Camilla Strang, Neil Ferguson, Anne Cori, et al
Volume
14
Issue
2
Pages
e1006885
DOI
https://dx.plos.org/10.1371/journal.ppat.1006885
Publisher URL
http://journals.plos.org/plospathogens/article?id=10.1371%2Fjournal.ppat.1006885
Scopus
85042693214
Mendeley
http://www.mendeley.com/research/pathogen-genome-sequences-informative-transmission-events
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"When are pathogen genome sequences informative of transmission events?", "type"=>"journal", "authors"=>[{"first_name"=>"Finlay", "last_name"=>"Campbell", "scopus_author_id"=>"57189970928"}, {"first_name"=>"Camilla", "last_name"=>"Strang", "scopus_author_id"=>"57200841442"}, {"first_name"=>"Neil", "last_name"=>"Ferguson", "scopus_author_id"=>"57096220000"}, {"first_name"=>"Anne", "last_name"=>"Cori", "scopus_author_id"=>"34874728300"}, {"first_name"=>"Thibaut", "last_name"=>"Jombart", "scopus_author_id"=>"24331843100"}], "year"=>2018, "source"=>"PLoS Pathogens", "identifiers"=>{"scopus"=>"2-s2.0-85042693214", "sgr"=>"85042693214", "doi"=>"10.1371/journal.ppat.1006885", "pui"=>"620981944", "pmid"=>"29420641", "isbn"=>"1111111111", "issn"=>"15537374"}, "id"=>"832bfbbc-6db6-3605-8e32-7b5724172cb5", "abstract"=>"Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data.", "link"=>"http://www.mendeley.com/research/pathogen-genome-sequences-informative-transmission-events", "reader_count"=>51, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>17, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>17, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>4, "Agricultural and Biological Sciences"=>21, "Medicine and Dentistry"=>6, "Veterinary Science and Veterinary Medicine"=>5, "Computer Science"=>1, "Immunology and Microbiology"=>4, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>21}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>4}, "Unspecified"=>{"Unspecified"=>5}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>5}}, "group_count"=>2}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85042693214"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85042693214?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85042693214&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=85042693214&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/85042693214", "dc:identifier"=>"SCOPUS_ID:85042693214", "eid"=>"2-s2.0-85042693214", "dc:title"=>"When are pathogen genome sequences informative of transmission events?", "dc:creator"=>"Campbell F.", "prism:publicationName"=>"PLoS Pathogens", "prism:issn"=>"15537366", "prism:eIssn"=>"15537374", "prism:volume"=>"14", "prism:issueIdentifier"=>"2", "prism:pageRange"=>nil, "prism:coverDate"=>"2018-02-01", "prism:coverDisplayDate"=>"February 2018", "prism:doi"=>"10.1371/journal.ppat.1006885", "citedby-count"=>"14", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"Imperial College London", "affiliation-city"=>"London", "affiliation-country"=>"United Kingdom"}], "pubmed-id"=>"29420641", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e1006885", "source-id"=>"4000151809", "openaccess"=>"1", "openaccessFlag"=>true}

Counter

  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"600", "xml_views"=>"14", "html_views"=>"1786"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"463", "xml_views"=>"5", "html_views"=>"505"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"132", "xml_views"=>"0", "html_views"=>"164"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"119", "xml_views"=>"1", "html_views"=>"214"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"59", "xml_views"=>"2", "html_views"=>"150"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"58", "xml_views"=>"0", "html_views"=>"106"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"65", "xml_views"=>"3", "html_views"=>"128"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"82", "xml_views"=>"0", "html_views"=>"152"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"67", "xml_views"=>"0", "html_views"=>"118"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"55", "xml_views"=>"0", "html_views"=>"140"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"50", "xml_views"=>"0", "html_views"=>"91"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"53", "xml_views"=>"0", "html_views"=>"111"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"78", "xml_views"=>"0", "html_views"=>"132"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"83", "xml_views"=>"1", "html_views"=>"150"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"68", "xml_views"=>"0", "html_views"=>"140"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"34", "xml_views"=>"0", "html_views"=>"119"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"39", "xml_views"=>"0", "html_views"=>"108"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"34", "xml_views"=>"0", "html_views"=>"78"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"50", "xml_views"=>"0", "html_views"=>"119"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"25", "xml_views"=>"0", "html_views"=>"83"}

PMC Usage Stats

  • {"unique-ip"=>"27", "full-text"=>"22", "pdf"=>"15", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"19", "full-text"=>"22", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"24", "full-text"=>"38", "pdf"=>"15", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"9", "cited-by"=>"1", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"20", "full-text"=>"20", "pdf"=>"11", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"13", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"18", "full-text"=>"18", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"20", "full-text"=>"26", "pdf"=>"41", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"19", "full-text"=>"26", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"14", "full-text"=>"20", "pdf"=>"12", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"26", "full-text"=>"22", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"15", "full-text"=>"20", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"23", "full-text"=>"25", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"9", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"16", "full-text"=>"19", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"9", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"21", "full-text"=>"22", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
Loading … Spinner
There are currently no alerts