Antibiotic resistance and factors associated with colonization dynamics of Staphylococcus aureus and Streptococcus pneumoniae in healthy children in Lima, Peru

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.