title: Population snapshot of Streptococcus pneumoniae causing invasive disease in South Africa prior to introduction of pneumococcal conjugate vaccines.
abstract: 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.
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa; Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council, Johannesburg, South Africa.
authors.forename: Kedibone M
authors.initials: KM
authors.lastname: Ndlangisa
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa; Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council, Johannesburg, South Africa.
authors.forename: Mignon
authors.initials: M
authors.lastname: du Plessis
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa; Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council, Johannesburg, South Africa.
authors.forename: Nicole
authors.initials: N
authors.lastname: Wolter
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa; Medical Research Council, Johannesburg, South Africa.
authors.forename: Linda
authors.initials: L
authors.lastname: de Gouveia
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa; Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia, United States of America.
authors.forename: Keith P
authors.initials: KP
authors.lastname: Klugman
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa; Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Medical Research Council, Johannesburg, South Africa.
authors.forename: Anne
authors.initials: A
authors.lastname: von Gottberg
authors.affiliation: Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.
mesh_terms: D000293:Adolescent; D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001483:Base Sequence; D002648:Child; D002675:Child, Preschool; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D058885:Multilocus Sequence Typing; D011008:Pneumococcal Infections / Q000188:drug therapy / Q000453:epidemiology*; D022242:Pneumococcal Vaccines / Q000276:immunology / Q000627:therapeutic use*; D017422:Sequence Analysis, DNA; D012703:Serotyping; D013019:South Africa / Q000453:epidemiology; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018074:Vaccines, Conjugate / Q000276:immunology / Q000627:therapeutic use*; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D022242:Pneumococcal Vaccines; D018074:Vaccines, Conjugate