title: Population structure, epidemiology and antibiotic resistance patterns of Streptococcus pneumoniae serotype 5: prior to PCV-13 vaccine introduction in Eastern Gambia.
abstract: BACKGROUND
  Streptococcus pneumoniae serotype 5 is among the most common serotypes causing invasive pneumococcal disease (IPD) in The Gambia. We anticipate that introduction of the 13-valent pneumococcal conjugate vaccine (PCV-13) into routine vaccination in The Gambia will reduce serotype 5 IPD. However, the emergence of new clones that have altered their genetic repertoire through capsular switching or genetic recombination after vaccination with PCV-13 poses a threat to this public health effort. In order to monitor for potential genetic changes post-PCV-13 vaccination, we established the baseline population structure, epidemiology, and antibiotic resistance patterns of serotype 5 before the introduction of PCV-13.
  
  
  METHODS
  Fifty-five invasive S. pneumoniae serotype 5 isolates were recovered from January 2009 to August 2011 in a population-based study in the Upper River Region of The Gambia. Serotyping was done by latex agglutination and confirmed by serotype-specific Polymerase Chain Reaction (PCR). Genotyping was undertaken using Multilocus Sequence Typing (MLST). Antimicrobial sensitivity was done using disc diffusion. Contingency table analyses were conducted using Pearson's Chi(2) and Fisher's exact test. Clustering was performed using Bionumerics version 6.5.
  
  
  RESULTS
  MLST resolved S. pneumoniae serotype 5 isolates into 3 sequence types (ST), namely ST 289(6/55), ST 3339(19/55) and ST 3404(30/55). ST 289 was identified as the major clonal complex. ST 3339, the prevalent genotype in 2009 [84.6% (11/13)], was replaced by ST 3404 [70.4% (19/27)] in 2010 as the dominant ST. Interestingly, ST 3404 showed lower resistance to tetracycline and oxacillin (P < 0.001), an empirical surrogate to penicillin in The Gambia.
  
  
  CONCLUSIONS
  There has been an emergence of ST 3404 in The Gambia prior to the introduction of PCV-13. Our findings provide important background data for future assessment of the impact of PCV-13 into routine immunization in developing countries, such as The Gambia.
authors.affiliation: Department of Biology, McMaster University, 1280 Main St. W, Hamilton, ON, L8S 4 K1, Canada. ashuebasi@yahoo.com.|Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia. ashuebasi@yahoo.com.
authors.forename: Eta E
authors.initials: EE
authors.lastname: Ashu
authors.affiliation: Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.
authors.forename: Sheikh
authors.initials: S
authors.lastname: Jarju
authors.affiliation: Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.
authors.forename: Michel
authors.initials: M
authors.lastname: Dione
authors.affiliation: Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.
authors.forename: Grant
authors.initials: G
authors.lastname: Mackenzie
authors.affiliation: Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.
authors.forename: Usman N
authors.initials: UN
authors.lastname: Ikumapayi
authors.affiliation: Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.|King Fahad Medical City, Central, 11525, Saudi Arabia.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Manjang
authors.affiliation: Center for Global Health and Health Policy, Global Health and Education Projects, P. O. BOX 234, Riverdale, MD, 20738, USA.
authors.forename: Romuladus
authors.initials: R
authors.lastname: Azuine
authors.affiliation: Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology / Q000627:therapeutic use; D016000:Cluster Analysis; D004352:Drug Resistance, Microbial; D005714:Gambia / Q000453:epidemiology; D005838:Genotype; D006801:Humans; D007841:Latex Fixation Tests; D058885:Multilocus Sequence Typing; D010068:Oxacillin / Q000494:pharmacology / Q000627:therapeutic use; D010406:Penicillins / Q000494:pharmacology / Q000627:therapeutic use; D011008:Pneumococcal Infections / Q000188:drug therapy / Q000453:epidemiology / Q000382:microbiology*; D022242:Pneumococcal Vaccines / Q000276:immunology; D015995:Prevalence; D065288:Serogroup; D013296:Streptococcus pneumoniae / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification*; D013752:Tetracycline / Q000494:pharmacology / Q000627:therapeutic use; D014611:Vaccination
chemical_list: C538862:13-valent pneumococcal vaccine; D000900:Anti-Bacterial Agents; D010406:Penicillins; D022242:Pneumococcal Vaccines; D013752:Tetracycline; D010068:Oxacillin
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