{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T04:00:55Z","timestamp":1791000055699,"version":"4.1.0"},"reference-count":42,"publisher":"Microbiology Society","issue":"12","license":[{"start":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T00:00:00Z","timestamp":1703030400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"crossref","award":["5U51IP000155"],"award-info":[{"award-number":["5U51IP000155"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014588","name":"Sanofi Pasteur","doi-asserted-by":"crossref","award":["PER00059"],"award-info":[{"award-number":["PER00059"]}],"id":[{"id":"10.13039\/100014588","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["D43TW011255"],"award-info":[{"award-number":["D43TW011255"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,20]]},"abstract":"<jats:p>\n                    Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.1747\" xlink:type=\"simple\">Bordetella pertussis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (\n                    <jats:italic>ptxP<\/jats:italic>\n                    ,\n                    <jats:italic>ptxA<\/jats:italic>\n                    ,\n                    <jats:italic>ptxB<\/jats:italic>\n                    ,\n                    <jats:italic>prn<\/jats:italic>\n                    and\n                    <jats:italic>fimH<\/jats:italic>\n                    ) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele\n                    <jats:italic>ptxP3<\/jats:italic>\n                    . The dominant genotype was\n                    <jats:italic>ptxP<\/jats:italic>\n                    3\n                    <jats:italic>-ptxA<\/jats:italic>\n                    1\n                    <jats:italic>-ptxB2-prn<\/jats:italic>\n                    2\n                    <jats:italic>-fimH<\/jats:italic>\n                    2 (31\/32, 96.9\u200a%), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9\u200a% (13\/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.1747\" xlink:type=\"simple\">B. pertussis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    disease, waning immunity due to the use of acellular vaccines and\/or population immunity gaps.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001162","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T12:17:10Z","timestamp":1703074630000},"source":"Crossref","is-referenced-by-count":7,"title":["Genomic characterization of Bordetella pertussis in South Africa, 2015\u20132019"],"prefix":"10.1099","volume":"9","author":[{"given":"Fahima","family":"Moosa","sequence":"first","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa"},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mignon","family":"du Plessis","sequence":"additional","affiliation":[{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa"},{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Weigand","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"}]},{"given":"Yanhui","family":"Peng","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"}]},{"given":"Dineo","family":"Mogale","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"de Gouveia","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta C.","family":"Nunes","sequence":"additional","affiliation":[{"name":"Department of Science and Technology\/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shabir A.","family":"Madhi","sequence":"additional","affiliation":[{"name":"Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa"},{"name":"South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather J.","family":"Zar","sequence":"additional","affiliation":[{"name":"Department of Pediatrics and Child Health, Red Cross Children\u2019s Hospital, Cape Town, South Africa; 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