title: Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013.
abstract: Serotype 1 is an important cause of invasive pneumococcal disease in South Africa and has declined following the introduction of the 13-valent pneumococcal conjugate vaccine in 2011. We genetically characterized 912 invasive serotype 1 isolates from 1989 to 2013. Simpson's diversity index (D) and recombination ratios were calculated. Factors associated with sequence types (STs) were assessed. Clonal complex 217 represented 96% (872/912) of the sampled isolates. Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), ST diversity increased in children <5 years (D, 0.39 to 0.63, P = 0.002) and individuals >14 years (D, 0.35 to 0.54, P < 0.001): ST-217 declined proportionately in children <5 years (153/203 [75%] versus 21/37 [57%], P = 0.027) and individuals >14 years (242/305 [79%] versus 96/148 [65%], P = 0.001), whereas ST-9067 increased (4/684 [0.6%] versus 24/228 [11%], P < 0.001). Three subclades were identified within ST-217: ST-217C1 (353/382 [92%]), ST-217C2 (15/382 [4%]), and ST-217C3 (14/382 [4%]). ST-217C2, ST-217C3, and single-locus variant (SLV) ST-8314 (20/912 [2%]) were associated with nonsusceptibility to chloramphenicol, tetracycline, and co-trimoxazole. ST-8314 (20/912 [2%]) was also associated with increased nonsusceptibility to penicillin (P < 0.001). ST-217C3 and newly reported ST-9067 had higher recombination ratios than those of ST-217C1 (4.344 versus 0.091, P < 0.001; and 0.086 versus 0.013, P < 0.001, respectively). Increases in genetic diversity were noted post-PCV13, and lineages associated with antimicrobial nonsusceptibility were identified.
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa mignond@nicd.ac.za.
authors.forename: Mignon
authors.identifier: 0000-0001-9186-0679
authors.initials: M
authors.lastname: du Plessis
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Mushal
authors.initials: M
authors.lastname: Allam
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
authors.forename: Stefano
authors.initials: S
authors.lastname: Tempia
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Nicole
authors.initials: N
authors.lastname: Wolter
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Linda
authors.initials: L
authors.lastname: de Gouveia
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Claire
authors.initials: C
authors.lastname: von Mollendorf
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.affiliation: Department of Medical Microbiology, Tshwane Academic Hospital, National Health Laboratory Service, Pretoria, South Africa.
authors.forename: Nontombi
authors.initials: N
authors.lastname: Mbelle
authors.affiliation: Department of Clinical Microbiology and Infectious Diseases, Chris Hani Baragwanath Academic Hospital, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Jeannette
authors.initials: J
authors.lastname: Wadula
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Cornick
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
authors.forename: Dean B
authors.initials: DB
authors.lastname: Everett
authors.affiliation: Streptococcus Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Lesley
authors.initials: L
authors.lastname: McGee
authors.affiliation: Emory Global Health Institute, Emory University, Atlanta, Georgia, USA.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Gladstone
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, 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, USA.
authors.forename: Keith P
authors.initials: KP
authors.lastname: Klugman
authors.affiliation: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Anne
authors.initials: A
authors.lastname: von Gottberg
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D005260:Female; D014644:Genetic Variation; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D010802:Phylogeny; D011008:Pneumococcal Infections / Q000453:epidemiology* / Q000382:microbiology*; D065288:Serogroup; D013019:South Africa / Q000453:epidemiology; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D055815:Young Adult