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

Pneumococcal conjugate vaccines (PCVs) have influenced population dynamics of <i>Streptococcus pneumoniae</i> in the nasopharynx and may have contributed to increased <i>Staphylococcus aureus</i> colonization. This study assessed the prevalence of colonization, antibiotic resistance patterns, and associated risk factors for colonization and co-colonization of <i>S. aureus</i> and <i>S. pneumoniae</i> 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 <i>S. aureus</i>, 20.3% with <i>S. pneumoniae</i>, and 2.9% co-colonized. Of the 176 <i>S. aureus</i> strains isolated, 1.7% were methicillin resistant and 20.5% were clindamycin resistant; no resistance to trimethoprim-sulfamethoxazole (SXT) was found. Among 182 <i>S. pneumoniae</i> 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 <i>S. aureus</i> colonization, while vaccination with PCV13 increased the prevalence of <i>S. pneumoniae</i> 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.