{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T23:23:36Z","timestamp":1792193016129,"version":"4.4.0"},"reference-count":47,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T00:00:00Z","timestamp":1712707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/AuthorWarrantyLicense.v1"},{"start":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T00:00:00Z","timestamp":1712707200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2024,4,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of\n              <jats:italic>Bordetella pertussis<\/jats:italic>\n              , the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA \u201cbaits\u201d targeting\n              <jats:italic>B. pertussis<\/jats:italic>\n              fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of\n              <jats:italic>B. pertussis<\/jats:italic>\n              genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of\n              <jats:italic>B. pertussis<\/jats:italic>\n              sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS\n              <jats:italic>481<\/jats:italic>\n              Ct &lt; 35 and &gt;10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/jcm.01653-23","type":"journal-article","created":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T14:02:16Z","timestamp":1709733736000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":12,"title":["Strengthening\n            <i>Bordetella pertussis<\/i>\n            genomic surveillance by direct sequencing of residual positive specimens"],"prefix":"10.1128","volume":"62","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0362-0099","authenticated-orcid":false,"given":"Yanhui","family":"Peng","sequence":"first","affiliation":[{"name":"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3168-1286","authenticated-orcid":false,"given":"Margaret M.","family":"Williams","sequence":"additional","affiliation":[{"name":"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9850-5175","authenticated-orcid":false,"given":"Lingzi","family":"Xiaoli","sequence":"additional","affiliation":[{"name":"ASRT Inc., Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2368-5313","authenticated-orcid":false,"given":"Ashley","family":"Simon","sequence":"additional","affiliation":[{"name":"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"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1434-3490","authenticated-orcid":false,"given":"Heather","family":"Fueston","sequence":"additional","affiliation":[{"name":"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4759-2985","authenticated-orcid":false,"given":"Maria L.","family":"Tondella","sequence":"additional","affiliation":[{"name":"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7278-0160","authenticated-orcid":true,"given":"Michael R.","family":"Weigand","sequence":"additional","affiliation":[{"name":"Division 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