Pneumococcal conjugate vaccines (PCVs) have influenced population dynamics of Streptococcus pneumoniae in the nasopharynx and may have contributed to increased Staphylococcus aureus colonization. This study assessed the prevalence of colonization, antibiotic resistance patterns, and associated risk factors for colonization and co-colonization of S. aureus and S. pneumoniae in healthy Peruvian children post-PCV introduction. Nasopharyngeal swabs from children <24 months were collected in five hospitals in Lima (2018–2019). Microbiological identification and antibiotic susceptibility tests were performed, and multinomial regression evaluated factors influencing colonization. Among 894 children, 19.7% were colonized with S. aureus, 20.3% with S. pneumoniae, and 2.9% co-colonized. Of the 176 S. aureus strains isolated, 1.7% were methicillin resistant and 20.5% were clindamycin resistant; no resistance to trimethoprim-sulfamethoxazole (SXT) was found. Among 182 S. pneumoniae strains isolated, 48.9% were resistant to macrolides, 74.7% to SXT; no resistance to penicillin was found. Breastfeeding and vaccination with PCV13 were associated with a reduced prevalence of S. aureus colonization, while vaccination with PCV13 increased the prevalence of S. pneumoniae colonization, mainly by non-vaccine serotypes. This study highlights the need to continue monitoring the changes in colonization dynamics and antimicrobial resistance patterns after vaccine introduction, to guide empirical therapy and future vaccine strategies.

We performed two different approaches (broth enrichment step prior to culture (BEC) and PCR (BEPCR)) for detecting Streptococcus pneumoniae from nasopharyngeal specimens collected from 242 children aged <6 years attending one hospital (n = 140) and one childcare centre (n = 102) in a major urban area in Brazil. These specimens were collected immediately before the introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) and the 13-valent vaccine (PCV13) for routine use in Brazil. Results were compared with previous findings obtained with direct culture (DC) on a selective medium. Colonisation prevalence was 58·3% (n = 141), being higher among children attending the childcare centre (62·7% vs. 55%). The culture-based methods (DC and BEC) enabled the detection of S. pneumoniae in 119 (49·2%) and 115 (47·5%) children, respectively. The PCR-based method (BEPCR) was more sensitive and 137 (56·6%) carriers were identified. Twenty-six serogroups/serotypes were identified, predominantly 6B, 19F, 14, 6A, 15C and 23F. Multiple colonisation was observed in 13 (5·4%) children. The estimated serotypes coverage of available PCVs was 40·4% for the 10-valent (included in the Brazilian immunisation programme) and 55·8% for the 13-valent (only available in private clinics). The use of robust approaches to obtain a more realistic insight about the asymptomatic carrier status is of paramount importance to estimate and assess the impact of vaccine implementation. The combination between culture-based and molecular methods constitutes a suitable strategy.