Persistence of Vaccine Serotype Carriage and Differences in Pneumococcal Carriage by Laboratory Method and Sample Type in Indigenous Individuals in the Southwest United States

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 aged <5 and >= 18 years 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 polymerase chain reaction [PCR]). Cultured Streptococcus pneumoniae was serotyped by sequencing. PCR-positive samples were serotyped by 13-valent pneumococcal conjugate vaccine (PCV13)-type PCR and TaqMan array card PCR. Results An overall 1503 participants were enrolled (age <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 when compared with cultured oropharyngeal swabs (0.6%) and nasopharyngeal swabs by culture (7.9%) or PCR (5.3%); PCV13-type carriage by any sample or method was 8.0%. Conclusions PCV13-type carriage persists in Indigenous populations. Use of molecular methods and oropharyngeal swabs for adults increased carriage prevalence estimates.