Key features of invasive pneumococcal isolates recovered in Lima, Peru determined through whole genome sequencing

Before PCV7 introduction, invasive pneumococcal disease (IPD) was responsible for approximately 12,000–18,000 deaths annually among children <5 years in Latin America. In Peru, PCV7 was introduced in 2009. We used whole genome sequencing to deduce key features of invasive strains collected in Lima, Peru from 2006 to 2011. We sequenced 212 IPD isolates from 16 hospitals in Lima pre (2006–2009; n = 133) and post (2010–2011; n = 79) PCV7 introduction; 130 (61.3%) isolates were from children ≤ 5 years old. CDC’s Streptococcus lab bioinformatics pipeline revealed serotypes, sequence types (STs), pilus genes, PBP types and other resistance determinants. During the pre-PCV7 period, serotype 14 was the most common serotype (24.8%), followed by 6 B (20.3%), 19F (10.5%), and 23F (6.8%). Post-PCV7, the proportion of PCV7 serotype 6 B decreased significantly (to 6.3%), while 19F (16.3%), 14 (15.0%), 23F (7.5%), and 19A (7.5%) were the most common serotypes; only serotypes 3 and 10A increased significantly. Overall, 82% (n = 173) of all isolates carried at least one resistance determinant, including 72 (34%) isolates that carried resistance determinants against 3 or more antimicrobial classes; of these 72 isolates, 56 (78%) belonged to a PCV7 serotype. Eighty-two STs were identified, with 53 of them organized in 14 clonal complexes. ST frequencies were distributed differently pre and post-PCV7 introduction, with only 18 of the 57 STs identified in years 2006–2009 isolates also observed in years 2010–2011 isolates. The apparent expansion of a 19F/ST1421 lineage with predicted β-lactam resistance (PBP type 13:16:20) and carrying resistance determinants against four additional antimicrobial classes was observed.