Abstract
Ocular infections have a substantial impact on global visual health. Despite their association with severe vision impairment, very few studies have systematically monitored antimicrobial resistance (AMR) over time using whole genome sequencing approaches. In the current study, we assembled 291 high-fidelity bacterial genomes isolated from patients attending a tertiary eye care centre in India, using long-read sequencing. Pseudomonas aeruginosa (n = 62) and Staphylococcus aureus (n = 60) were the most common pathogens in the cohort, with more than 45% of isolates exhibiting multidrug resistance and more than 15% classified as extensively drug-resistant. Genotype–phenotype analyses and multilocus sequence typing revealed a previously unreported mecA-negative methicillin-resistant Staphylococcus aureus strain, ST9578, resistant to vancomycin and teicoplanin. Potential AMR mechanisms, like a mutation in the 23S rRNA gene associated with linezolid resistance and a KorB-like protein-encoding gene associated with fluoroquinolone resistance, were identified using comparative genomics. This is the first large-scale genomic surveillance effort focused on ocular pathogens in the Indian subcontinent and the potential AMR mechanisms and sequence types identified underscore the need for larger such studies in low-and-middle-income countries.
Data availability
All genomes assembled as part of this work are openly available to researchers across the world and can be accessed at NCBI (PRJNA1267791) and https://doi.org/10.5281/zenodo.1899625467. The source data used for generating the figures is available in the folder ‘Supplementary data 10’ provided along with this paper.
Code availability
The custom Python scripts are available at https://github.com/apuratha/ocular-amr, https://github.com/Shyamili09/ARGs-Antibiogram-comparison and https://doi.org/10.5281/zenodo.1900054968.
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Tallapaka, K. Genomic insights into antimicrobial resistance in ocular pathogens from India. Zenodo https://doi.org/10.5281/zenodo.19000549.
Acknowledgements
The study was made possible by funding from the Rockefeller Foundation (Grant 2021 HTH 018). We acknowledge Prof. L S Shashidhara for his guidance. Hyderabad Eye Research Foundation (HERF) for facilitating project execution. The HPC facility of CCMB is acknowledged for providing computational resources for data analysis.
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K.B.T., J.J. and D.T.S. conceived and designed the study. B.B. & P.G. clinically examined the patients. L.L. performed antimicrobial susceptibility testing and DNA extraction. R.B. and S.A. carried out library preparation and sequencing. V.S.K., A.R.P., A.K. and R.J.M. conducted the bioinformatics analysis. A.P. performed comparative genome analysis. V.S.K. prepared the first draft of the manuscript, which was reviewed and edited by K.B.T., J.J., D.T.S., P.G., B.B. and V.K.N. Ar.P. was responsible for project management. All authors read and approved the final manuscript.
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Kumar, V.S., Pandiyan, A., Bhagat, R. et al. Genomic insights into antimicrobial resistance in ocular pathogens from India. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09952-w
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DOI: https://doi.org/10.1038/s42003-026-09952-w
