Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
- Publication Date
- February 04, 2014
- Journal
- PLOS ONE
- Authors
- Pimlapas Leekitcharoenphon, Eva M. Nielsen, Rolf S. Kaas, Ole Lund, et al
- Volume
- 9
- Issue
- 2
- Pages
- e87991
- DOI
- https://dx.plos.org/10.1371/journal.pone.0087991
- Publisher URL
- http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0087991
- PubMed
- http://www.ncbi.nlm.nih.gov/pubmed/24505344
- PubMed Central
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913712
- Europe PMC
- http://europepmc.org/abstract/MED/24505344
- Web of Science
- 000336971300028
- Scopus
- 84895096959
- Mendeley
- http://www.mendeley.com/research/evaluation-whole-genome-sequencing-outbreak-detection-salmonella-enterica-6
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CiteULike | Further Information
- {"link"=>{"url"=>"http://www.citeulike.org/user/heathervincent/article/13049517"}, "post_time"=>"2014-02-14 08:58:43", "tag"=>["snp", "wgs"], "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pone.0087991"}, "username"=>"heathervincent", "article_id"=>"13049517"}
- {"link"=>{"url"=>"http://www.citeulike.org/user/aprasad/article/13775563"}, "post_time"=>"2015-09-26 01:15:27", "tag"=>["foodborn_outbreak", "outbreak_tracking", "salmonella"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pone.0087991"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/24505344"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=24505344"}], "username"=>"aprasad", "article_id"=>"13775563"}
Mendeley | Further Information
{"title"=>"Evaluation of whole genome sequencing for outbreak detection of salmonella enterica", "type"=>"journal", "authors"=>[{"first_name"=>"Pimlapas", "last_name"=>"Leekitcharoenphon", "scopus_author_id"=>"36617619400"}, {"first_name"=>"Eva M.", "last_name"=>"Nielsen", "scopus_author_id"=>"35478560500"}, {"first_name"=>"Rolf S.", "last_name"=>"Kaas", "scopus_author_id"=>"51763770700"}, {"first_name"=>"Ole", "last_name"=>"Lund", "scopus_author_id"=>"7103226268"}, {"first_name"=>"Frank M.", "last_name"=>"Aarestrup", "scopus_author_id"=>"7005978857"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84895096959", "sgr"=>"84895096959", "pui"=>"372510249", "isbn"=>"1932-6203", "pmid"=>"24505344", "doi"=>"10.1371/journal.pone.0087991"}, "id"=>"7633e6fd-df0c-3df2-b537-40b51f8915b8", "abstract"=>"Salmonella enterica is a common cause of minor and large food borne outbreaks. To achieve successful and nearly 'real-time' monitoring and identification of outbreaks, reliable sub-typing is essential. Whole genome sequencing (WGS) shows great promises for using as a routine epidemiological typing tool. Here we evaluate WGS for typing of S. Typhimurium including different approaches for analyzing and comparing the data. A collection of 34 S. Typhimurium isolates was sequenced. This consisted of 18 isolates from six outbreaks and 16 epidemiologically unrelated background strains. In addition, 8 S. Enteritidis and 5 S. Derby were also sequenced and used for comparison. A number of different bioinformatics approaches were applied on the data; including pan-genome tree, k-mer tree, nucleotide difference tree and SNP tree. The outcome of each approach was evaluated in relation to the association of the isolates to specific outbreaks. The pan-genome tree clustered 65% of the S. Typhimurium isolates according to the pre-defined epidemiology, the k-mer tree 88%, the nucleotide difference tree 100% and the SNP tree 100% of the strains within S. Typhimurium. The resulting outcome of the four phylogenetic analyses were also compared to PFGE revealing that WGS typing achieved the greater performance than the traditional method. In conclusion, for S. Typhimurium, SNP analysis and nucleotide difference approach of WGS data seem to be the superior methods for epidemiological typing compared to other phylogenetic analytic approaches that may be used on WGS. These approaches were also superior to the more classical typing method, PFGE. Our study also indicates that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data and whole genome sequencing results.", "link"=>"http://www.mendeley.com/research/evaluation-whole-genome-sequencing-outbreak-detection-salmonella-enterica-6", "reader_count"=>186, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>34, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>54, "Student > Postgraduate"=>3, "Student > Master"=>41, "Other"=>13, "Student > Bachelor"=>25, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>34, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>54, "Student > Postgraduate"=>3, "Student > Master"=>41, "Other"=>13, "Student > Bachelor"=>25, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Agricultural and Biological Sciences"=>98, "Veterinary Science and Veterinary Medicine"=>3, "Chemistry"=>1, "Computer Science"=>7, "Economics, Econometrics and Finance"=>1, "Engineering"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>34, "Mathematics"=>3, "Medicine and Dentistry"=>19, "Social Sciences"=>2, "Immunology and Microbiology"=>10}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>19}, "Social Sciences"=>{"Social Sciences"=>2}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>2}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>10}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>98}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>34}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"New Zealand"=>2, "Canada"=>2, "Sweden"=>1, "Belgium"=>1, "United States"=>4, "Ireland"=>1, "Denmark"=>3, "United Kingdom"=>1, "Australia"=>1, "Germany"=>2, "India"=>1, "Spain"=>1}, "group_count"=>13}CrossRef
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Scopus | Further Information
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- {"id"=>"431032039606079488", "text"=>"SNP and ANI measurements better than k-mer and pan-genome approaches for clustering Salmonella using WGS: http://t.co/jNAsOBuQJv", "created_at"=>"2014-02-05T11:50:21Z", "user"=>"pathogenomenick", "user_name"=>"Nick Loman", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1370766780/215282_10150165068141692_502431691_6652059_5392675_n_normal.jpg"}
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- {"id"=>"431059921996881920", "text"=>"RT @pathogenomenick: SNP and ANI measurements better than k-mer and pan-genome approaches for clustering Salmonella using WGS: http://t.co/…", "created_at"=>"2014-02-05T13:41:08Z", "user"=>"m_swistak", "user_name"=>"Marcin Świstak", "user_profile_image"=>"http://pbs.twimg.com/profile_images/426508163517411328/lIg_y4ce_normal.jpeg"}
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- {"id"=>"431087525734924289", "text"=>"Nice paper from the Danes on using different phylo/strain similarity methods for investigating Salmonella outbreaks http://t.co/jEnhzg0HiU", "created_at"=>"2014-02-05T15:30:50Z", "user"=>"flashton2003", "user_name"=>"Phil Ashton", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1246355309/180391_10150128098886061_508261060_8635743_7953409_n_normal.jpg"}
- {"id"=>"431088080184176641", "text"=>"RT @flashton2003: Nice paper from the Danes on using different phylo/strain similarity methods for investigating Salmonella outbreaks http:…", "created_at"=>"2014-02-05T15:33:02Z", "user"=>"CJernberg", "user_name"=>"Cecilia Jernberg", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3375400660/930b0e5611f5d67cef4619343157b596_normal.jpeg"}
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- {"id"=>"431167096412590080", "text"=>"RT @pathogenomenick: SNP and ANI measurements better than k-mer and pan-genome approaches for clustering Salmonella using WGS: http://t.co/…", "created_at"=>"2014-02-05T20:47:01Z", "user"=>"snacktavish", "user_name"=>"Emily Jane McTavish", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000167043682/dbd7cfeca09be9db57c6a9dc1a3ea02a_normal.jpeg"}
- {"id"=>"431431021150871552", "text"=>"RT @pathogenomenick: SNP and ANI measurements better than k-mer and pan-genome approaches for clustering Salmonella using WGS: http://t.co/…", "created_at"=>"2014-02-06T14:15:45Z", "user"=>"91Mattmoore", "user_name"=>"Matt Moore", "user_profile_image"=>"http://pbs.twimg.com/profile_images/422309182788730880/xEoHbqrg_normal.jpeg"}
- {"id"=>"434011258841751553", "text"=>"This paper found up to 30 SNPs of variation within outbreaks of Salmonella Typhimurium http://t.co/jEnhzg0HiU", "created_at"=>"2014-02-13T17:08:42Z", "user"=>"flashton2003", "user_name"=>"Phil Ashton", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1246355309/180391_10150128098886061_508261060_8635743_7953409_n_normal.jpg"}
- {"id"=>"434014766718537728", "text"=>"RT @flashton2003: This paper found up to 30 SNPs of variation within outbreaks of Salmonella Typhimurium http://t.co/jEnhzg0HiU", "created_at"=>"2014-02-13T17:22:38Z", "user"=>"winstanley_c", "user_name"=>"Craig Winstanley", "user_profile_image"=>"http://pbs.twimg.com/profile_images/3480597464/c5455e496c3ae6e99bec56dca4cc564d_normal.jpeg"}
- {"id"=>"434019206687121408", "text"=>"RT @flashton2003: This paper found up to 30 SNPs of variation within outbreaks of Salmonella Typhimurium http://t.co/jEnhzg0HiU", "created_at"=>"2014-02-13T17:40:17Z", "user"=>"91Mattmoore", "user_name"=>"Matt Moore", "user_profile_image"=>"http://pbs.twimg.com/profile_images/422309182788730880/xEoHbqrg_normal.jpeg"}
- {"id"=>"434236531956781056", "text"=>"RT @flashton2003: This paper found up to 30 SNPs of variation within outbreaks of Salmonella Typhimurium http://t.co/jEnhzg0HiU", "created_at"=>"2014-02-14T08:03:51Z", "user"=>"heathermvincent", "user_name"=>"Heather Vincent", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000817625426/146365bd97bec4330a75e0b34f7ad3d1_normal.jpeg"}
- {"id"=>"445935264947380224", "text"=>"“Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica“\nhttp://t.co/iIFqc9hkJU", "created_at"=>"2014-03-18T14:50:26Z", "user"=>"infoecho", "user_name"=>"Jason Chin", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1355717194/image_normal.jpg"}
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Counter
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PMC Usage Stats | Further Information
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Relative Metric
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