Eleonora Cella, Catherine G Sutcliffe, Lindsay R Grant, Carol Tso, Robert C Weatherholtz, Shea Littlepage, Ladonna Becenti, Mohammad Jubair, Brenna C Simons, Marcella Harker-Jones, Raymond Reid, Del Yazzie, Mathuram Santosham, Katherine L O'Brien, Laura L Hammitt, Taj Azarian
{"title":"2001-2018 年接种疫苗时代的肺炎链球菌血清 3 型群体结构。","authors":"Eleonora Cella, Catherine G Sutcliffe, Lindsay R Grant, Carol Tso, Robert C Weatherholtz, Shea Littlepage, Ladonna Becenti, Mohammad Jubair, Brenna C Simons, Marcella Harker-Jones, Raymond Reid, Del Yazzie, Mathuram Santosham, Katherine L O'Brien, Laura L Hammitt, Taj Azarian","doi":"10.1099/mgen.0.001196","DOIUrl":null,"url":null,"abstract":"<p><p><b>Background.</b> Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001-2009 and 6.2/100 000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100 000 to 2.3/100 000.<b>Methods.</b> We analysed the genomic epidemiology of serotype 3 isolates collected from 129 adults and 63 children with pneumococcal carriage (<i>n</i>=61) or IPD (<i>n</i>=131) from 2001 to 2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in serotype 3 population structure over time.<b>Results.</b> The serotype 3 population structure was characterized by three dominant subpopulations: <i>clade II</i> (<i>n</i>=90, 46.9 %) and <i>clade Iα</i> (<i>n</i>=59, 30.7 %), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (<i>n</i>=43, 22.4 %). The proportion of <i>clade II</i>-associated IPD cases increased significantly from 2001 to 2010 to 2011-2018 among adults (23.1-71.8 %; <i>P</i><0.001) but not in children (27.3-33.3 %; <i>P</i>=0.84). Over the same period, the proportion of <i>clade II-</i>associated carriage increased; this was statistically significant among children (23.3-52.6 %; <i>P</i>=0.04) but not adults (0-50.0 %, <i>P</i>=0.08).<b>Conclusions.</b> In this setting with persistent serotype 3 IPD and carriage, <i>clade II</i> has increased since 2010. Genomic changes may be contributing to the observed trends in serotype 3 carriage and disease over time.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 3","pages":""},"PeriodicalIF":4.0000,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963907/pdf/","citationCount":"0","resultStr":"{\"title\":\"<i>Streptococcus pneumoniae</i> serotype 3 population structure in the era of conjugate vaccines, 2001-2018.\",\"authors\":\"Eleonora Cella, Catherine G Sutcliffe, Lindsay R Grant, Carol Tso, Robert C Weatherholtz, Shea Littlepage, Ladonna Becenti, Mohammad Jubair, Brenna C Simons, Marcella Harker-Jones, Raymond Reid, Del Yazzie, Mathuram Santosham, Katherine L O'Brien, Laura L Hammitt, Taj Azarian\",\"doi\":\"10.1099/mgen.0.001196\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><b>Background.</b> Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001-2009 and 6.2/100 000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100 000 to 2.3/100 000.<b>Methods.</b> We analysed the genomic epidemiology of serotype 3 isolates collected from 129 adults and 63 children with pneumococcal carriage (<i>n</i>=61) or IPD (<i>n</i>=131) from 2001 to 2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in serotype 3 population structure over time.<b>Results.</b> The serotype 3 population structure was characterized by three dominant subpopulations: <i>clade II</i> (<i>n</i>=90, 46.9 %) and <i>clade Iα</i> (<i>n</i>=59, 30.7 %), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (<i>n</i>=43, 22.4 %). The proportion of <i>clade II</i>-associated IPD cases increased significantly from 2001 to 2010 to 2011-2018 among adults (23.1-71.8 %; <i>P</i><0.001) but not in children (27.3-33.3 %; <i>P</i>=0.84). Over the same period, the proportion of <i>clade II-</i>associated carriage increased; this was statistically significant among children (23.3-52.6 %; <i>P</i>=0.04) but not adults (0-50.0 %, <i>P</i>=0.08).<b>Conclusions.</b> In this setting with persistent serotype 3 IPD and carriage, <i>clade II</i> has increased since 2010. Genomic changes may be contributing to the observed trends in serotype 3 carriage and disease over time.</p>\",\"PeriodicalId\":18487,\"journal\":{\"name\":\"Microbial Genomics\",\"volume\":\"10 3\",\"pages\":\"\"},\"PeriodicalIF\":4.0000,\"publicationDate\":\"2024-03-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963907/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Microbial Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1099/mgen.0.001196\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbial Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1099/mgen.0.001196","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001-2018.
Background. Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001-2009 and 6.2/100 000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100 000 to 2.3/100 000.Methods. We analysed the genomic epidemiology of serotype 3 isolates collected from 129 adults and 63 children with pneumococcal carriage (n=61) or IPD (n=131) from 2001 to 2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in serotype 3 population structure over time.Results. The serotype 3 population structure was characterized by three dominant subpopulations: clade II (n=90, 46.9 %) and clade Iα (n=59, 30.7 %), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (n=43, 22.4 %). The proportion of clade II-associated IPD cases increased significantly from 2001 to 2010 to 2011-2018 among adults (23.1-71.8 %; P<0.001) but not in children (27.3-33.3 %; P=0.84). Over the same period, the proportion of clade II-associated carriage increased; this was statistically significant among children (23.3-52.6 %; P=0.04) but not adults (0-50.0 %, P=0.08).Conclusions. In this setting with persistent serotype 3 IPD and carriage, clade II has increased since 2010. Genomic changes may be contributing to the observed trends in serotype 3 carriage and disease over time.
期刊介绍:
Microbial Genomics (MGen) is a fully open access, mandatory open data and peer-reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.