Ocular Microbiology and Immunology Group
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2026 OMIG Abstract

Genomic Characterization and Antimicrobial Resistance Profile of Streptococcus pneumoniae from Ocular Infections

Fernando H. A. Murata, Ana Lucía Meléndez, and Paulo J. M Bispo

Department of Ophthalmology, Mass Eye and Ear (MEE), Harvard Medical School, Boston, Massachusetts

Purpose: Streptococcus pneumoniae (SPN) is a leading cause of ocular infections with evidence suggesting distinct microscale biogeographies across ocular tissues. Given the global spread of non-vaccine serotypes and multidrug-resistant (MDR) lineages, comprehensive genomic characterization is critical to understand tissue tropism and MDR emergence and inform the development of novel preventive and therapeutic strategies. This study investigates the population structure and antimicrobial resistance (AMR) profiles of ocular SPN, correlating specific genetic lineages with clinical manifestations.

Methods: A total of 104 non-duplicate SPN clinical isolates were recovered from patients at MEE (2018-2025). Following Oxford Nanopore sequencing, genomes were analyzed via Pathogenwatch for serotyping, AMR profiling, and GPSC assignment. Minimum inhibitory concentrations (MICs) were determined by broth microdilution.

Results: Conjunctivitis was diagnosed in 49 (47.1%) patients, followed by keratitis (34, 32.7%), endophthalmitis (11, 10.6%), and other ocular conditions (10, 9.6%). Non-encapsulated lineages accounted for 45 isolates (43.3%) and were associated with 83.7% of conjunctivitis cases. On the other hand, most isolates causing keratitis, endophthalmitis and orbital/lacrimal system infections were encapsulated (46, 83.6%%), with 20 distinct serotypes identified. Pneumococcal Conjugate Vaccine (PCV) 21 offers the broadest coverage for encapsulated strains (71.7%), driven primarily by the inclusion of 23A, 11A, and 23B. PCV20 covers 37%, PCV15 17.4% and PCV13 only 8.7%. GPSC60 was the most frequent cluster (43, 41.3%), strongly correlating with non-encapsulates strains (97.7%), while GPSC3 and GPSC7 were the most identified cluster in the encapsulated lineages (15.7%, each). Phenotypic resistance to macrolides was high, with 57.7% of isolates resistant to erythromycin and 55.8% to azithromycin; this profile was corroborated by the prevalence of resistance markers (mef(A)/msr(D): 47.1%; ermB: 8.6%), predominantly found in non-encapsulated strains (71.4%). Tetracycline resistance markers (tetM variants) were identified in 34 (32.7%) isolates (42.3% phenotypically resistant). Conversely, high susceptibility was observed for beta-lactams (100%), fluoroquinolones (99.0%), and chloramphenicol (96.1%).

Conclusions: SPN genomic lineages demonstrated to have distinct ocular tissue tropism, with encapsulated strains linked to sight-threatening diseases, whereas non-encapsulated lineages predominate in conjunctivitis and carry a higher burden of macrolide resistance. The prevalence of these resistant, non-encapsulated strains as well as encapsulated strains that form a highly diverse population at the serotype level is a public health concern as they evade most conjugate vaccines currently recommended in the US national immunization program, underscoring the need for continuous genomic surveillance.