{"corpus_id":7974237,"paper_sha":"b4cb1329de461f7e6c5e438e6ff32e46ae12f544","doi":"10.1371/journal.pone.0132623","arxiv_id":null,"pmid":26182210,"pmcid":"4504479","mag_id":2141958765,"dblp_id":null,"acl_id":null,"title":"Genetic Variation of Bordetella pertussis in Austria","year":2015,"publication_date":"2015-07-16","venue":"PLoS ONE","journal":{"name":"PLoS ONE","pages":null,"volume":"10"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle"],"pubmed_pub_types":["Journal Article","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Medicine"],"reference_count":50,"citation_count":21,"influential_citation_count":1,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Adolescent","mj":false,"ui":"D000293"},{"d":"Adult","mj":false,"ui":"D000328"},{"d":"Austria","mj":false,"qs":[{"q":"epidemiology","mj":false,"ui":"Q000453"}],"ui":"D001317"},{"d":"Bacterial Proteins","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D001426"},{"d":"Bacterial Typing Techniques","mj":false,"ui":"D015373"},{"d":"Base Sequence","mj":false,"ui":"D001483"},{"d":"Bordetella pertussis","mj":false,"qs":[{"q":"classification","mj":false,"ui":"Q000145"},{"q":"genetics","mj":true,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"},{"q":"pathogenicity","mj":false,"ui":"Q000472"}],"ui":"D001886"},{"d":"Child","mj":false,"ui":"D002648"},{"d":"Child, Preschool","mj":false,"ui":"D002675"},{"d":"DNA, Bacterial","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"},{"q":"immunology","mj":false,"ui":"Q000276"},{"q":"isolation & purification","mj":false,"ui":"Q000302"}],"ui":"D004269"},{"d":"Female","mj":false,"ui":"D005260"},{"d":"Fimbriae Proteins","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D036781"},{"d":"Gene 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Subunits","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D021122"},{"d":"Transcription Factors","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D014157"},{"d":"Vaccination","mj":false,"ui":"D014611"},{"d":"Virulence Factors, Bordetella","mj":false,"qs":[{"q":"genetics","mj":false,"ui":"Q000235"},{"q":"metabolism","mj":false,"ui":"Q000378"}],"ui":"D010566"},{"d":"Whooping Cough","mj":false,"qs":[{"q":"epidemiology","mj":false,"ui":"Q000453"},{"q":"immunology","mj":false,"ui":"Q000276"},{"q":"microbiology","mj":false,"ui":"Q000382"},{"q":"prevention & control","mj":true,"ui":"Q000517"}],"ui":"D014917"}],"chemicals":[{"n":"Bacterial Proteins","ui":"D001426","reg":"0"},{"n":"DNA, Bacterial","ui":"D004269","reg":"0"},{"n":"Pertussis Vaccine","ui":"D010567","reg":"0"},{"n":"Protein Subunits","ui":"D021122","reg":"0"},{"n":"Transcription Factors","ui":"D014157","reg":"0"},{"n":"Virulence Factors, Bordetella","ui":"D010566","reg":"0"},{"n":"bvgS protein, Bordetella pertussis","ui":"C080662","reg":"0"},{"n":"fimD protein, Bordetella","ui":"C489284","reg":"0"},{"n":"tracheal colonization factor, Bordetella pertussis","ui":"C096309","reg":"0"},{"n":"Fimbriae Proteins","ui":"D036781","reg":"147680-16-8"},{"n":"Pertussis Toxin","ui":"D037342","reg":"EC 2.4.2.31"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0132623&type=printable","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/b4cb1329de461f7e6c5e438e6ff32e46ae12f544","s2_open_access_license":"CCBY","s2_open_access_status":"GOLD","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"In Austria, vaccination coverage against Bordetella pertussis infections during infancy is estimated at around 90%. Within the last years, however, the number of pertussis cases has increased steadily, not only in children but also in adolescents and adults, indicating both insufficient herd immunity and vaccine coverage. Waning immunity in the host and/or adaptation of the bacterium to the immunised hosts could contribute to the observed re-emergence of pertussis. In this study we therefore addressed the genetic variability in B. pertussis strains from several Austrian cities. Between the years 2002 and 2008, 110 samples were collected from Vienna (n = 32), Linz (n = 63) and Graz (n = 15) by nasopharyngeal swabs. DNA was extracted from the swabs, and bacterial sequence polymorphisms were examined by MLVA (multiple-locus variable number of tandem repeat analysis) (n = 77), by PCR amplification and conventional Sanger sequencing of the polymorphic regions of the prn (pertactin) gene (n = 110), and by amplification refractory mutation system quantitative PCR (ARMS-qPCR) (n = 110) to directly address polymorphisms in the genes encoding two pertussis toxin subunits (ptxA and ptxB), a fimbrial adhesin (fimD), tracheal colonisation factor (tcfA), and the virulence sensor protein (bvgS). Finally, the ptxP promoter region was screened by ARMS-qPCR for the presence of the ptxP3 allele, which has been associated with elevated production of pertussis toxin. The MLVA analysis revealed the highest level of polymorphisms with an absence of MLVA Type 29, which is found outside Austria. Only Prn subtypes Prn1/7, Prn2 and Prn3 were found with a predominance of the non-vaccine type Prn2. The analysis of the ptxA, ptxB, fimD, tcfA and bvgS polymorphisms showed a genotype mixed between the vaccine strain Tohama I and a clinical isolate from 2006 (L517). The major part of the samples (93%) displayed the ptxP3 allele. The consequences for the vaccination strategy are discussed.","claims":[{"public_id":"cl_aa870c535de917b53be3364c544b6841","status":"active","text":"Austrian Bordetella pertussis isolates showed substantial genetic variability across multiple loci and an absence of MLVA type 29.","confidence":0.97,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_aa870c535de917b53be3364c544b6841"},{"public_id":"cl_5558aec0153d0d08fc644dbc9fed0d16","status":"active","text":"Only Prn1/7, Prn2, and Prn3 subtypes were detected, with Prn2 predominating among the isolates.","confidence":0.98,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_5558aec0153d0d08fc644dbc9fed0d16"},{"public_id":"cl_db260fe710f4581394680a9bf4536f96","status":"active","text":"Polymorphisms in ptxA, ptxB, fimD, tcfA, and bvgS formed a genotype intermediate between the vaccine strain Tohama I and the clinical isolate L517.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_db260fe710f4581394680a9bf4536f96"},{"public_id":"cl_9244efbc4b22f56b354ccbba258186a7","status":"active","text":"The ptxP3 allele was present in 93% of the samples.","confidence":0.99,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous 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(12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_562658f70a103269638a936df26a106f"},{"public_id":"co_5f3a9e0741ca9dc2d24a56f648861107","status":"active","name":"genetic variability","description":"Differences in genetic markers and sequence polymorphisms observed among bacterial isolates.","types":["property"],"aliases":["genetic variation"],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/concepts/co_5f3a9e0741ca9dc2d24a56f648861107"},{"public_id":"co_8ad2fcf4badab325c613e9c4918cf92f","status":"active","name":"Prn2","description":"A pertactin subtype identified among the isolates and reported as the predominant non-vaccine type.","types":["genetic subtype"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous 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