Our ongoing 14-year surveillance (2006-2020) in Rochester NY has tracked pneumococcal serotypes causing acute otitis media (AOM) in children age 6-36 months.
Pneumococci were identified by culture of middle ear fluid using tympanocentesis and nasopharyngeal swabs. Serotypes were determined by Quellung and whole genome sequencing (WGS) (using Illumina NextSeq500 or Pacific Biosciences RSII). Assemblies of 35B strains were aligned using LR216049 as reference. A dot plot was used to map overall sequence similarity between “old 35B” isolated prior to 2015 and “new 35B” isolated after 2015.
Serotype 35B case/carriage ratio of old 35B was 0.13 and 1.17 for new 35B, p=0.0001, suggesting increased virulence. New 35B accounts for almost 25% of all pneumococcal isolates from children with AOM, MLST was the same for old and new 35B strains (type 558). 2149 genes were consistently identified among 39 strains of 35B with WGS. Specifically WGS alignments revealed a 20 kb region encoding 30 proteins that was inverted in the old 35B (2 strains) strains compared to the new 35B (3 strains). Further analysis is ongoing.
35B has emerged as a dominant otopathogen in recent years among children in Rochester NY. Increased virulence appears associated with genomic change.