Pneumococcal Carriage Among Indigenous Children in the Southwest United States in 2022-2023

Indigenous children in the Southwest United States are disproportionately affected by pneumococcal disease compared with the general population. The prevalence of pediatric pneumococcal carriage by culture in 2015-2017 in the Southwest was 49.5%. Since then, pandemic-related changes in pathogen circulation have occurred, and new pneumococcal vaccines were introduced, potentially altering pneumococcal carriage. This study was conducted to estimate carriage prevalence and serotype distribution among children <5 years of age in the Southwest in 2022-2023.

Indigenous children in the Southwest 7-59 months old were enrolled in a cross-sectional study in 2022-2023. A nasopharyngeal swab was collected and tested for Streptococcus pneumoniae by enrichment culture and polymerase chain reaction (PCR) for lytA and piaB genes. Samples were considered PCR positive if both targets had a cycle threshold <40. Serotypes were determined by whole-genome sequencing of cultured isolates.

Among 498 available samples from 500 enrolled children, pneumococcus was detected in 338 (67.9%) by culture or PCR (40.8% by culture and 67.5% by PCR). In a multivariable model, more children <6 years old in the household and asthma were significantly associated with increased carriage prevalence. Carriage prevalence by culture was significantly lower than in 2015-2017 (40.8% vs. 49.5%; P = 0.004). Based on serotyping 204 isolates, 19.6% were PCV15 and 39.2% were PCV20-type serotypes.

Carriage prevalence by culture was lower compared with prepandemic in these communities. Many serotypes are covered by higher valency vaccines, which have the potential to reduce carriage and disease in Indigenous children.