Persistence of vaccine serotype carriage and differences in pneumococcal carriage by lab method and sample type in Indigenous individuals in the Southwest USA.

Background: In the United States, the invasive pneumococcal disease incidence in Indigenous populations is higher than in the general population. Molecular detection and/or specimen sampling from multiple body sites could enhance our understanding of pneumococcal carriage, a prerequisite for disease.

Methods: Persons <5 and ≥18 years of age from the Navajo Nation and White Mountain Apache Tribal lands were enrolled in an observational carriage study from October 2015 through September 2017. Swabs from the nasopharynx (all participants) and oropharynx (adults only) were collected and tested by enriched culture or molecular methods (lytA and piaB PCR). Cultured Streptococcus pneumoniae were serotyped by sequencing. PCR-positive samples were serotyped by PCV13-type PCR and TaqMan Array Card (TAC PCR).

Results: 1503 participants enrolled (<5 years: n=600; ≥18 years: n=903). Among children, pneumococcal positivity was similar by culture (49.5%) and PCR (50.8%); PCV13-type carriage was 8.0% by any method. Among adults, oropharyngeal swab positivity by PCR was 18.5%, an increase compared to cultured oropharyngeal swabs (0.6%) and to nasopharyngeal swabs by culture (7.9%) or PCR 5.3%); PCV13-type carriage by any sample or method was 8.0%.

Discussion: PCV13-type carriage persists in Indigenous populations. Use of molecular methods and oropharyngeal swabs for adults increased carriage prevalence estimates.