Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001-2018

BackgroundDespite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 (ST3) continues to cause disease among Indigenous communities in the Southwest US. In the Navajo Nation, ST3 IPD incidence increased among adults (3.8/100,000 in 2001-2009 and 6.2/100,000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100,000 to 2.3/100,000. MethodsWe analyzed the genomic epidemiology of ST3 isolates collected from 129 adults and 63 children with pneumococcal carriage (n=61) or IPD (n=131) from 2001-2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in ST3 population structure over time. ResultsThe ST3 population structure was characterized by three dominant subpopulations: clade II (n=90, 46.9%) and clade I (n=59, 30.7%), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (n=43, 22.4%). The proportion of clade II-associated IPD cases increased significantly from 2001-2010 to 2011-2018 among adults (23.1% to 71.8%; p<0.001) but not in children (27.3% to 33.3%; p=0.84). Over the same period, the proportion of clade II- associated carriage increased; this was statistically significant among children (23.3% to 52.6%; p=0.04) but not adults (0% to 50.0%, p=0.08). ConclusionsIn this setting with persistent ST3 IPD and carriage, clade II has increased since 2010. Genomic changes may be contributing to the observed trends in ST3 carriage and disease over time.