title: Pre-vaccination nasopharyngeal pneumococcal carriage in a Nigerian population: epidemiology and population biology.
abstract: BACKGROUND
  Introduction of pneumococcal vaccines in Nigeria is a priority as part of the Accelerated Vaccine Introduction Initiative (AVI) of the Global Alliance for Vaccines and Immunisation (GAVI). However, country data on the burden of pneumococcal disease (IPD) is limited and coverage by available conjugate vaccines is unknown. This study was carried out to describe the pre vaccination epidemiology and population biology of pneumococcal carriage in Nigeria.
  
  
  METHODS
  This was a cross sectional survey. Nasopharyngeal swabs (NPS) were obtained from a population sample in 14 contiguous peri-urban Nigerian communities. Data on demographic characteristics and risk factor for carriage were obtained from all study participants. Pneumococci isolated from NPS were characterised by serotyping, antimicrobial susceptibility and Multi Locus Sequencing Typing (MLST).
  
  
  RESULTS
  The prevalence of pneumococcal carriage was 52.5%. Carriage was higher in children compared to adults (67.4% vs. 26%), highest (≈90%) in infants aged <9 months and reduced significantly with increasing age (P<0.001). Serotypes 19F (18.6%) and 6A (14.4%) were most predominant. Potential vaccine coverage was 43.8%, 45.0% and 62% for PCV-7, PCV-10 and PCV-13 respectively. There were 16 novel alleles, 72 different sequence types (STs) from the isolates and 3 Sequence Types (280, 310 and 5543) were associated with isolates of more than one serotype indicative of serotype switching. Antimicrobial resistance was high for cotrimoxazole (93%) and tetracycline (84%), a third of isolates had intermediate resistance to penicillin. Young age was the only risk factor significantly associated with carriage.
  
  
  CONCLUSIONS
  Pneumococcal carriage and serotype diversity is highly prevalent in Nigeria especially in infants. Based on the coverage of serotypes in this study, PCV-13 is the obvious choice to reduce disease burden and prevalence of drug resistant pneumococci. However, its use will require careful monitoring. Our findings provide sound baseline data for impact assessment following vaccine introduction in Nigeria.
authors.affiliation: Medical Research Council Unit, The Gambia, Fajara, The Gambia.
authors.forename: Ifedayo M O
authors.initials: IM
authors.lastname: Adetifa
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
authors.forename: Christy A N
authors.initials: CA
authors.lastname: Okoromah
authors.forename: Chinelo
authors.initials: C
authors.lastname: Ebruke
authors.forename: Victor
authors.initials: V
authors.lastname: Inem
authors.forename: David
authors.initials: D
authors.lastname: Nsekpong
authors.forename: Abdoulie
authors.initials: A
authors.lastname: Bojang
authors.forename: Richard A
authors.initials: RA
authors.lastname: Adegbola
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002353:Carrier State / Q000453:epidemiology* / Q000382:microbiology; D002648:Child; D002675:Child, Preschool; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D009305:Nasopharynx / Q000382:microbiology*; D009549:Nigeria / Q000453:epidemiology; D011008:Pneumococcal Infections / Q000453:epidemiology* / Q000517:prevention & control*; D022242:Pneumococcal Vaccines / Q000627:therapeutic use*; D011153:Population; D015995:Prevalence; D013296:Streptococcus pneumoniae / Q000302:isolation & purification*; D013997:Time Factors; D014611:Vaccination / Q000379:methods / Q000706:statistics & numerical data; D055815:Young Adult
chemical_list: D022242:Pneumococcal Vaccines