Ocular S. pneumoniae

S. pneumoniae isolated from 2014 to 2017 from 45 separate ocular infections were characterized by genome sequencing. S. pneumoniae were mainly isolated from keratitis (n=21, 46.7%) or conjunctivitis (n=15, 33.3%). Non-typeable Epidemic Conjunctivitis Cluster (ECC) strains (9/15; 60%) were the most common causes of conjunctivitis, with ST448 (8/15; 53.3%) being most frequently identified. Conversely, S. pneumoniae keratitis were caused by a highly diverse population of isolates grouping within 13 different clonal complex. As revealed by capsular serotyping, most of the conjunctivitis S. pneumoniae strains (12/15; 80%) were unencapsulated whereas S. pneumoniae causing keratitis were predominantly encapsulated (20/21; 95.2%). In our sample, 95.5% (43/45) of the isolates were non-vaccine types. Carriage of macrolide resistance genes was the most common (20/45; 44.4%), and usually associated with the mefA+msrD (n=15) genotype. The percentage of macrolide resistant isolates increased over the period of our study from 30.8% in 2014 to 56.3% in 2017. Interestingly, our data demonstrates that strains grouped within the ECC are highly adapted and confined to the conjunctival mucosa only. Keratitis is caused by a highly diverse population of S. pneumoniae that escape the current vaccine designs. These data will be useful in informing the design of next generation vaccines.