{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T08:07:03Z","timestamp":1785830823176,"version":"3.56.0"},"reference-count":64,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T00:00:00Z","timestamp":1748908800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T00:00:00Z","timestamp":1748908800000},"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":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,6,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Despite widespread vaccination, pertussis (caused by\n                      <jats:italic toggle=\"yes\">Bordetella pertussis<\/jats:italic>\n                      ) persists in many countries, frequently causing outbreaks and severe cases in infants. The resurgence of pertussis may be due to genetic changes in the vaccine antigens of circulating\n                      <jats:italic toggle=\"yes\">B. pertussis<\/jats:italic>\n                      strains. However, current typing methods, which depend on bacterial cultures, hinder our understanding of\n                      <jats:italic toggle=\"yes\">B. pertussis<\/jats:italic>\n                      genotypes, especially in developing countries. This study aimed to analyze vaccine antigen-based genotypic variants (\n                      <jats:italic toggle=\"yes\">ptxP<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">ptxA<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">fim3<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">prn<\/jats:italic>\n                      ) of\n                      <jats:italic toggle=\"yes\">B. pertussis<\/jats:italic>\n                      in Peru from 2018 to 2019 via direct Sanger sequencing of nasopharyngeal swabs (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 96). PCR-based sequencing was successful for the genes\n                      <jats:italic toggle=\"yes\">ptxP<\/jats:italic>\n                      in 86% (83\/96),\n                      <jats:italic toggle=\"yes\">ptxA<\/jats:italic>\n                      in 100% (96\/96),\n                      <jats:italic toggle=\"yes\">fim3<\/jats:italic>\n                      in 75% (72\/96), and\n                      <jats:italic toggle=\"yes\">prn<\/jats:italic>\n                      in 68% (65\/96) of the samples. The\n                      <jats:italic toggle=\"yes\">ptxP3<\/jats:italic>\n                      variant was found in 100% (83\/83),\n                      <jats:italic toggle=\"yes\">ptxA1<\/jats:italic>\n                      in 100% (96\/96),\n                      <jats:italic toggle=\"yes\">fim3-1<\/jats:italic>\n                      in 97.3% (70\/72),\n                      <jats:italic toggle=\"yes\">fim3-2<\/jats:italic>\n                      in 2.7% (2\/72), and\n                      <jats:italic toggle=\"yes\">prn2<\/jats:italic>\n                      in 100% (65\/65) of the samples. Sixty-three samples yielded a complete allelic profile, with genotype VI (\n                      <jats:italic toggle=\"yes\">ptxP3-ptxA1-fim3-1-prn2<\/jats:italic>\n                      ) predominating nationwide (96.8%), mainly in Lima (29.5%), Amazonas (13.1%), Callao (11.5%), and La Libertad (11.5%). Genotype VII (\n                      <jats:italic toggle=\"yes\">ptxP3-ptxA1-fim3-2-prn2<\/jats:italic>\n                      ) was less common (3.2%), found in Lima (50%) and Callao (50%). The predominance and expansion of genotype VI suggested the presence of biological traits linked to infection, possibly due to the\n                      <jats:italic toggle=\"yes\">ptxP3<\/jats:italic>\n                      allele, such as high respiratory colonization or increased pertussis toxin production, which could potentially increase disease transmission and severity. These findings will facilitate Peru\u2019s ability to monitor and control\n                      <jats:italic toggle=\"yes\">B. pertussis<\/jats:italic>\n                      , improving public health responses and reducing the outbreak incidence and severity.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Despite widespread vaccination, pertussis (caused by\n                      <jats:italic toggle=\"yes\">Bordetella pertussis<\/jats:italic>\n                      ) still causes severe outbreaks in infants worldwide. Genetic changes in the vaccine antigens of\n                      <jats:italic toggle=\"yes\">B. pertussis<\/jats:italic>\n                      strains may drive this resurgence. Current culture-based typing methods limit our understanding of these genotypes, particularly in developing countries. This study provides valuable insights into the genotypic variability of\n                      <jats:italic toggle=\"yes\">B. pertussis<\/jats:italic>\n                      in Peru from 2018 to 2019, employing an isolation-free genotyping method allowing the direct Sanger sequencing of vaccine antigen genes from clinical samples. These findings can enhance public health decision-making by improving our understanding of the genetic changes that drive severe pertussis outbreaks, particularly in developing countries that use whole-cell vaccines. This knowledge enables rapid outbreak responses, improved vaccine strategies, and strengthened surveillance, prevention, and control measures.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.02004-24","type":"journal-article","created":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T09:00:12Z","timestamp":1747213212000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Vaccine antigen-based genotyping of\n                    <i>Bordetella pertussis<\/i>\n                    by direct Sanger sequencing of clinical samples in Peru from 2018 to 2019"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6843-3206","authenticated-orcid":true,"given":"Eduardo","family":"Juscamayta-L\u00f3pez","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03gx6zj11","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Nacional de Salud P\u00fablica, Instituto Nacional de Salud","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Betsab\u00e9","family":"Vega-Abad","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03gx6zj11","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Nacional de Salud P\u00fablica, Instituto Nacional de Salud","place":["Lima, Peru"]},{"name":"Facultad de Ciencias Biol\u00f3gicas, Universidad Nacional Mayor de San Marcos","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faviola","family":"Valdivia","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03gx6zj11","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Nacional de Salud P\u00fablica, Instituto Nacional de Salud","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda P\u00eda","family":"Soto","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03gx6zj11","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Nacional de Salud P\u00fablica, Instituto Nacional de Salud","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Horna","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03gx6zj11","id-type":"ROR","asserted-by":"publisher"}],"name":"Centro Nacional de Salud P\u00fablica, Instituto Nacional de Salud","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Garc\u00eda-de-la-Guarda","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias Biol\u00f3gicas, Universidad Nacional Mayor de San Marcos","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30390-0"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.5935\/0103-507X.20190029"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2017.07.015"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2019.1694395"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-014-2297-2"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-016-2655-3"},{"key":"e_1_3_3_8_2","unstructured":"Ministerio de Salud. 2018. Norma T\u00e9cnica de Salud N\u00b0141- MINSA\/2018\/DIGIESP Norma T\u00e9cnica de Salud que establece el Esquema Nacional de Vacunaci\u00f3n"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofad325"},{"key":"e_1_3_3_10_2","unstructured":"Centro Nacional de Epidemiolog\u00eda. 2019. Prevenci\u00f3n y Control de Enfermedades\/Ministerio de Salud de Per\u00fa. Alerta Epidemiol\u00f3gica No AE-010-2019."},{"key":"e_1_3_3_11_2","unstructured":"Centro Nacional de Epidemiolog\u00eda. 2023. Prevenci\u00f3n y Control de Enfermedades\/Ministerio de Salud de Per\u00fa. Alerta Epidemiol\u00f3gica No AE-CDC-No 12-2023."},{"key":"e_1_3_3_12_2","unstructured":"Centro Nacional de Epidemiolog\u00eda. 2021. Prevenci\u00f3N y Control de Enfermedades\/Ministerio de Salud de Per\u00fa. N\u00famero de casos de tos ferina Per\u00fa 2016 \u2013 2021."},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00601-11"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-29773-9"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-019-3869-7"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13052-024-01753-3"},{"key":"e_1_3_3_17_2","unstructured":"World Health Organization. 2014. Laboratory manual for the diagnosis of whooping cough caused by Bordetella pertussis\/Bordetella parapertussis: update 2014."},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1508.081511"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2672.2012.05299.x"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.9.5520-5528.2001"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0046407"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0046407"},{"key":"e_1_3_3_23_2","unstructured":"European Centre for Disease Prevention and Control. 2022. ECDC technical report. Stockholm ECDC."},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2012.01.001"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01189-14"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268818002303"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2511.190329"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2004.131478"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12941-021-00458-3"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2304.161575"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001162"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0066150"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2016.06.052"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01074-14"},{"key":"e_1_3_3_35_2","unstructured":"Montilla Escudero EA. 2017. Caracterizaci\u00f3n molecular de Bordetella pertussis en Colombia 1995-2014 MSc thesis"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/CVI.00294-06"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.001042"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/CVI.00717-13"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0031985"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2019.1587315"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2019.24.7.1700832"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2805.211958"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2706.203850"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2014.09.068"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018014"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268813000071"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abn3253"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2021.104970"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu665"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2022.2077129"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-016-1700-2"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00430-017-0524-z"},{"key":"e_1_3_3_53_2","first-page":"1","article-title":"Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran","volume":"12","author":"Saedi S","year":"2020","unstructured":"Saedi S, Safarchi A, Noofeli M, Tadayon K, Tay ACY, Lamichhane B, Rahimi H, Shahcheraghi F. 2020. Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran. Iran J Microbiol 12:1\u201310.","journal-title":"Iran J Microbiol"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2203.151136"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2504.180812"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0077165"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000180"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-84409-0"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid3001.221588"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.000688"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02036-12"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2703.202314"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1177\/03000605221078782"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2010.00257.x"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep12888"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02004-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02004-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T09:02:53Z","timestamp":1748941373000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.02004-24"}},"subtitle":[],"editor":[{"given":"Rebekah M.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,6,3]]},"references-count":64,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,6,3]]}},"alternative-id":["10.1128\/spectrum.02004-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.02004-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,3]]},"assertion":[{"value":"2024-08-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-30","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-05-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02004-24"}}