Population snapshot of Streptococcus pneumoniae causing invasive disease in South Africa prior to introduction of pneumococcal conjugate vaccines
We determined the sequence types of isolates that caused invasive pneumococcal disease (IPD) prior to routine use of pneumococcal conjugate vaccines (PCV) in South Africa. PCV-13 serotypes and 6C isolates collected in 2007 (1 461/2 437, 60%) from patients of all ages as part of on-going, national, l...
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| Veröffentlicht in: | PloS one 2014-09, Vol.9 (9), p.e107666 |
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| description | We determined the sequence types of isolates that caused invasive pneumococcal disease (IPD) prior to routine use of pneumococcal conjugate vaccines (PCV) in South Africa. PCV-13 serotypes and 6C isolates collected in 2007 (1 461/2 437, 60%) from patients of all ages as part of on-going, national, laboratory-based surveillance for IPD, were selected for genetic characterization. In addition, all 134 non-PCV isolates from children |
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PCV-13 serotypes and 6C isolates collected in 2007 (1 461/2 437, 60%) from patients of all ages as part of on-going, national, laboratory-based surveillance for IPD, were selected for genetic characterization. In addition, all 134 non-PCV isolates from children <2 years were selected for characterization. Sequence type diversity by serotype and age category (children <5 years vs. individuals ≥5 years) was assessed for PCV serotypes using Simpson's index of diversity. Similar genotypes circulated among isolates from children and adults and the majority of serotypes were heterogeneous. While globally disseminated clones were common among some serotypes (e.g., serotype 1 [clonal complex (CC) 217, 98% of all serotype 1] and 14 [CC230, 43%)]), some were represented mainly by clonal complexes rarely reported elsewhere (e.g., serotype 3 [CC458, 60%] and 19A [CC2062, 83%]). In children <2 years, serotype 15B and 8 were the most common serotypes among non-PCV isolates (16% [22/134] and 15% [20/134] isolates, respectively). Sequence type 7052 and 53 were most common among serotypes 15B and 8 isolates and accounted for 58% (7/12) and 64% (9/14) of the isolates, respectively. Serotype 19F, 14, 19A and 15B had the highest proportions of penicillin non-susceptible isolates. Genotypes rarely reported in other parts of the world but common among some of our serotypes highlight the importance of our data as these genotypes may emerge post PCV introduction.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0107666</identifier><identifier>PMID: 25233455</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adolescent ; Adult ; Adults ; Anti-Bacterial Agents - pharmacology ; Antibiotics ; Base Sequence ; Biology and Life Sciences ; Child ; Child, Preschool ; Children ; DNA, Bacterial - analysis ; DNA, Bacterial - genetics ; Female ; Genotypes ; Humans ; Immunization ; Laboratories ; Male ; Medicine and Health Sciences ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Penicillin ; Penicillins ; Pneumococcal Infections - drug therapy ; Pneumococcal Infections - epidemiology ; Pneumococcal Vaccines - immunology ; Pneumococcal Vaccines - therapeutic use ; Pneumonia ; Sequence Analysis, DNA ; Serotypes ; Serotyping ; South Africa - epidemiology ; Streptococcus infections ; Streptococcus pneumoniae ; Streptococcus pneumoniae - classification ; Streptococcus pneumoniae - genetics ; Streptococcus pneumoniae - isolation & purification ; Vaccines ; Vaccines, Conjugate - immunology ; Vaccines, Conjugate - therapeutic use ; Young Adult</subject><ispartof>PloS one, 2014-09, Vol.9 (9), p.e107666</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Ndlangisa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2014 Ndlangisa et al 2014 Ndlangisa et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-f4fe128628e8f7972d1fdbad8dec51433a8ca322d3e68bdd91adc6134e7bb84e3</citedby><cites>FETCH-LOGICAL-c692t-f4fe128628e8f7972d1fdbad8dec51433a8ca322d3e68bdd91adc6134e7bb84e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169438/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169438/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25233455$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Esposito, Susanna</contributor><creatorcontrib>Ndlangisa, Kedibone M</creatorcontrib><creatorcontrib>du Plessis, Mignon</creatorcontrib><creatorcontrib>Wolter, Nicole</creatorcontrib><creatorcontrib>de Gouveia, Linda</creatorcontrib><creatorcontrib>Klugman, Keith P</creatorcontrib><creatorcontrib>von Gottberg, Anne</creatorcontrib><creatorcontrib>GERMS-SA</creatorcontrib><title>Population snapshot of Streptococcus pneumoniae causing invasive disease in South Africa prior to introduction of pneumococcal conjugate vaccines</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>We determined the sequence types of isolates that caused invasive pneumococcal disease (IPD) prior to routine use of pneumococcal conjugate vaccines (PCV) in South Africa. PCV-13 serotypes and 6C isolates collected in 2007 (1 461/2 437, 60%) from patients of all ages as part of on-going, national, laboratory-based surveillance for IPD, were selected for genetic characterization. In addition, all 134 non-PCV isolates from children <2 years were selected for characterization. Sequence type diversity by serotype and age category (children <5 years vs. individuals ≥5 years) was assessed for PCV serotypes using Simpson's index of diversity. Similar genotypes circulated among isolates from children and adults and the majority of serotypes were heterogeneous. While globally disseminated clones were common among some serotypes (e.g., serotype 1 [clonal complex (CC) 217, 98% of all serotype 1] and 14 [CC230, 43%)]), some were represented mainly by clonal complexes rarely reported elsewhere (e.g., serotype 3 [CC458, 60%] and 19A [CC2062, 83%]). In children <2 years, serotype 15B and 8 were the most common serotypes among non-PCV isolates (16% [22/134] and 15% [20/134] isolates, respectively). Sequence type 7052 and 53 were most common among serotypes 15B and 8 isolates and accounted for 58% (7/12) and 64% (9/14) of the isolates, respectively. Serotype 19F, 14, 19A and 15B had the highest proportions of penicillin non-susceptible isolates. Genotypes rarely reported in other parts of the world but common among some of our serotypes highlight the importance of our data as these genotypes may emerge post PCV introduction.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Adults</subject><subject>Anti-Bacterial Agents - pharmacology</subject><subject>Antibiotics</subject><subject>Base Sequence</subject><subject>Biology and Life Sciences</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Children</subject><subject>DNA, Bacterial - analysis</subject><subject>DNA, Bacterial - genetics</subject><subject>Female</subject><subject>Genotypes</subject><subject>Humans</subject><subject>Immunization</subject><subject>Laboratories</subject><subject>Male</subject><subject>Medicine and Health Sciences</subject><subject>Microbial Sensitivity Tests</subject><subject>Multilocus Sequence Typing</subject><subject>Penicillin</subject><subject>Penicillins</subject><subject>Pneumococcal Infections - drug therapy</subject><subject>Pneumococcal Infections - epidemiology</subject><subject>Pneumococcal Vaccines - immunology</subject><subject>Pneumococcal Vaccines - therapeutic use</subject><subject>Pneumonia</subject><subject>Sequence Analysis, DNA</subject><subject>Serotypes</subject><subject>Serotyping</subject><subject>South Africa - epidemiology</subject><subject>Streptococcus infections</subject><subject>Streptococcus pneumoniae</subject><subject>Streptococcus pneumoniae - classification</subject><subject>Streptococcus pneumoniae - genetics</subject><subject>Streptococcus pneumoniae - isolation & purification</subject><subject>Vaccines</subject><subject>Vaccines, Conjugate - immunology</subject><subject>Vaccines, Conjugate - therapeutic use</subject><subject>Young Adult</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9-K1DAUxoso7jr6BqIBQfBixqZJ0_RGGBb_DCysOOptSJOTmQydpibpoI_hG5vZ6S5TUJBetJz8zndOvp6TZc9xvsCkwm93bvCdbBe962CR47xijD3ILnFNijkrcvLw7PsiexLCLs9Lwhl7nF0UZUEILcvL7Pdn1w-tjNZ1KHSyD1sXkTNoHT300Smn1BBQ38Gwd52VgJQcgu02yHYHGewBkLYBZIAUQGs3xC1aGm-VRL23zqPo0kH0Tg_qtkaSPokdlWWLlOt2w0ZGQAeplO0gPM0eGdkGeDa-Z9m3D--_Xn2aX998XF0tr-eK1UWcG2oAF5wVHLip6qrQ2OhGaq5BlZgSIrmSpCg0AcYbrWsstWKYUKiahlMgs-zlSbdvXRCjm0HgkpGccl5ViVidCO3kTqT77KX_JZy04jbg_EZIH61qQTBmDIW6JrlqKDekLqGmlANtQBJijtXejdWGZg9aQTJFthPR6Ulnt2LjDoJiVlPCk8CrUcC7HwOE-I-WR2ojU1e2My6Jqb0NSiwp5pjwMjU5yxZ_odKjYW_THwFjU3yS8GaSkJgIP-MmzUIQq_WX_2dvvk_Z12fsFmQbt8G1w3FUwhSkJ1B5F4IHc-8czsVxHe7cEMd1EOM6pLQX567fJ93NP_kDqQAKnA</recordid><startdate>20140918</startdate><enddate>20140918</enddate><creator>Ndlangisa, Kedibone M</creator><creator>du Plessis, Mignon</creator><creator>Wolter, Nicole</creator><creator>de Gouveia, Linda</creator><creator>Klugman, Keith P</creator><creator>von Gottberg, Anne</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20140918</creationdate><title>Population snapshot of Streptococcus pneumoniae causing invasive disease in South Africa prior to introduction of pneumococcal conjugate vaccines</title><author>Ndlangisa, Kedibone M ; du Plessis, Mignon ; Wolter, Nicole ; de Gouveia, Linda ; Klugman, Keith P ; von Gottberg, Anne</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-f4fe128628e8f7972d1fdbad8dec51433a8ca322d3e68bdd91adc6134e7bb84e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Adults</topic><topic>Anti-Bacterial Agents - 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PCV-13 serotypes and 6C isolates collected in 2007 (1 461/2 437, 60%) from patients of all ages as part of on-going, national, laboratory-based surveillance for IPD, were selected for genetic characterization. In addition, all 134 non-PCV isolates from children <2 years were selected for characterization. Sequence type diversity by serotype and age category (children <5 years vs. individuals ≥5 years) was assessed for PCV serotypes using Simpson's index of diversity. Similar genotypes circulated among isolates from children and adults and the majority of serotypes were heterogeneous. While globally disseminated clones were common among some serotypes (e.g., serotype 1 [clonal complex (CC) 217, 98% of all serotype 1] and 14 [CC230, 43%)]), some were represented mainly by clonal complexes rarely reported elsewhere (e.g., serotype 3 [CC458, 60%] and 19A [CC2062, 83%]). In children <2 years, serotype 15B and 8 were the most common serotypes among non-PCV isolates (16% [22/134] and 15% [20/134] isolates, respectively). Sequence type 7052 and 53 were most common among serotypes 15B and 8 isolates and accounted for 58% (7/12) and 64% (9/14) of the isolates, respectively. Serotype 19F, 14, 19A and 15B had the highest proportions of penicillin non-susceptible isolates. Genotypes rarely reported in other parts of the world but common among some of our serotypes highlight the importance of our data as these genotypes may emerge post PCV introduction.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25233455</pmid><doi>10.1371/journal.pone.0107666</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Adolescent Adult Adults Anti-Bacterial Agents - pharmacology Antibiotics Base Sequence Biology and Life Sciences Child Child, Preschool Children DNA, Bacterial - analysis DNA, Bacterial - genetics Female Genotypes Humans Immunization Laboratories Male Medicine and Health Sciences Microbial Sensitivity Tests Multilocus Sequence Typing Penicillin Penicillins Pneumococcal Infections - drug therapy Pneumococcal Infections - epidemiology Pneumococcal Vaccines - immunology Pneumococcal Vaccines - therapeutic use Pneumonia Sequence Analysis, DNA Serotypes Serotyping South Africa - epidemiology Streptococcus infections Streptococcus pneumoniae Streptococcus pneumoniae - classification Streptococcus pneumoniae - genetics Streptococcus pneumoniae - isolation & purification Vaccines Vaccines, Conjugate - immunology Vaccines, Conjugate - therapeutic use Young Adult |
| title | Population snapshot of Streptococcus pneumoniae causing invasive disease in South Africa prior to introduction of pneumococcal conjugate vaccines |
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