{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T23:23:34Z","timestamp":1792193014586,"version":"4.4.0"},"reference-count":28,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T00:00:00Z","timestamp":1722902400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/AuthorWarrantyLicense.v1"},{"start":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T00:00:00Z","timestamp":1722902400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000030","name":"HHS | Centers for Disease Control and Prevention","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,8,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      In the United States, the general laboratory method for diagnosing pertussis, caused by\n                      <jats:italic>Bordetella pertussis,<\/jats:italic>\n                      is real-time PCR (rt-PCR) targeting insertion sequence 481 (IS\n                      <jats:italic>481<\/jats:italic>\n                      ). Other\n                      <jats:italic>Bordetella<\/jats:italic>\n                      species (\n                      <jats:italic>parapertussis, holmesii<\/jats:italic>\n                      , and\n                      <jats:italic>bronchiseptica<\/jats:italic>\n                      ) can also cause a pertussis-like syndrome, and some commercial laboratory assays include the insertion sequence 1001 (pIS\n                      <jats:italic>1001<\/jats:italic>\n                      ) that can detect\n                      <jats:italic>B. parapertussis<\/jats:italic>\n                      \/\n                      <jats:italic>B. bronchiseptica (BppBb<\/jats:italic>\n                      ). Because IS\n                      <jats:italic>481<\/jats:italic>\n                      exists in\n                      <jats:italic>B. pertussis<\/jats:italic>\n                      and\n                      <jats:italic>B. holmesii<\/jats:italic>\n                      , current commercial assays cannot differentiate these two species. We used a multiplex rt-PCR assay containing species-specific targets to\n                      <jats:italic>Bordetella<\/jats:italic>\n                      to evaluate clinical specimens detected as\n                      <jats:italic>B. pertussis<\/jats:italic>\n                      \/\n                      <jats:italic>B. holmesii<\/jats:italic>\n                      (\n                      <jats:italic>BpBh<\/jats:italic>\n                      ) or\n                      <jats:italic>BppBb<\/jats:italic>\n                      by commercial laboratories. A sample of 3,984 clinical specimens positive for IS\n                      <jats:italic>481<\/jats:italic>\n                      or pIS\n                      <jats:italic>1001<\/jats:italic>\n                      from two commercial laboratories during 2012\u20132019 were re-tested at CDC. Agreement of\n                      <jats:italic>Bordetella<\/jats:italic>\n                      species between the CDC and commercial laboratory assays, and the proportion of commercial laboratory specimens that were non-\n                      <jats:italic>B<\/jats:italic>\n                      .\n                      <jats:italic>pertussis<\/jats:italic>\n                      by CDC\u2019s assay was assessed. Overall agreement in\n                      <jats:italic>Bordetella<\/jats:italic>\n                      species detection and identification between the CDC and commercial lab assays was 85%. Agreement for identifying\n                      <jats:italic>B. pertussis<\/jats:italic>\n                      was 87% for 3,663\n                      <jats:italic>BpBh<\/jats:italic>\n                      specimens and 98% for identifying\n                      <jats:italic>B. parapertussis<\/jats:italic>\n                      in 310\n                      <jats:italic>BppBb<\/jats:italic>\n                      specimens. CDC\u2019s assay detected\n                      <jats:italic>B. holmesii<\/jats:italic>\n                      in 55\/3,984 (1.4%) specimens. Most discrepant results (410\/490, 82%) were\n                      <jats:italic>BpBh<\/jats:italic>\n                      specimens interpreted as indeterminate\n                      <jats:italic>B. pertussis<\/jats:italic>\n                      at CDC. We found a small portion of\n                      <jats:italic>B. holmesii<\/jats:italic>\n                      in a sample of IS\n                      <jats:italic>481<\/jats:italic>\n                      -positive clinical specimens originally identified by commercial laboratory rt-PCR assays, suggesting that commercial PCR assays are a reliable diagnostic tool for correctly identifying\n                      <jats:italic>Bordetella<\/jats:italic>\n                      species in most patients with suspected pertussis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      When testing specimens collected from patients with suspected pertussis, large-scale commercial laboratories in the United States employ an IS\n                      <jats:italic>481<\/jats:italic>\n                      -based assay that cannot differentiate between\n                      <jats:italic>Bordetella pertussis<\/jats:italic>\n                      and\n                      <jats:italic>Bordetella holmseii<\/jats:italic>\n                      . The level of\n                      <jats:italic>B. holmesii<\/jats:italic>\n                      causing pertussis-like illness in the United States is not well-understood given that only\n                      <jats:italic>B. pertussis<\/jats:italic>\n                      is nationally notifiable. After re-testing with a multiplex, species-specific rt-PCR assay, our data show low levels of\n                      <jats:italic>B. holmesii<\/jats:italic>\n                      identified in a sample of IS\n                      <jats:italic>481<\/jats:italic>\n                      -positive clinical specimens originally identified by commercial laboratory rt-PCR assays. These results reinforce the validity of large-scale commercial rt-PCR testing as a reliable diagnostic tool for pertussis in the United States.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00783-24","type":"journal-article","created":{"date-parts":[[2024,7,9]],"date-time":"2024-07-09T09:02:05Z","timestamp":1720515725000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":13,"title":["Comparison of\n                    <i>Bordetella<\/i>\n                    species identification among differing rt-PCR assays in the United States"],"prefix":"10.1128","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9205-9055","authenticated-orcid":true,"given":"Matthew","family":"Cole","sequence":"first","affiliation":[{"name":"Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley K.","family":"Simon","sequence":"additional","affiliation":[{"name":"Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda","family":"Faulkner","sequence":"additional","affiliation":[{"name":"Oregon Health Authority, Portland, Oregon, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tami","family":"Skoff","sequence":"additional","affiliation":[{"name":"Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria L.","family":"Tondella","sequence":"additional","affiliation":[{"name":"Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clemente","family":"Montero","sequence":"additional","affiliation":[{"name":"Quest Diagnostics, San Juan Capistrano, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melinda B.","family":"Nye","sequence":"additional","affiliation":[{"name":"Labcorp, Burlington, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret","family":"Williams","sequence":"additional","affiliation":[{"name":"Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm7003a2"},{"key":"e_1_3_3_3_2","unstructured":"Centers for Disease Control and Prevention. 2017. 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