Temporal trends and shifting mycological spectrum of infectious keratitis in Egypt before, during and after the COVID-19 pandemic: a four-year laboratory-based surveillance study

Fungal keratitis (FK) significantly contributes to corneal morbidity in tropical and subtropical environments; yet, longitudinal data describing post-pandemic epidemiologic changes remain limited. This study evaluated temporal trends and changes in the mycological spectrum of culture-confirmed FK in Egypt before, during and after the COVID-19 era. We retrospectively inspected corneal scrapings collected between January 2019 and December 2022 at a major ophthalmic hospital in the Nile Delta, Egypt. Specimens were examined by direct microscopy and culture. Temporal patterns in fungal positivity, seasonal variation, species distribution and diversity were compared across pre-pandemic, pandemic, and post-pandemic periods. Of 584 specimens analyzed, 423 (72.4%) yielded microbial growth, and fungi accounted for 97.6% (413/423) of culture-positive isolates. The proportion of fungal-positive specimens increased from 49.0% pre-pandemic to 67.6% during the pandemic and 79.7% in the post-pandemic period ( p < 0.001). In multivariable analysis, rural residence (aOR = 2.32, 95% CI: 1.53–3.53), history of ocular trauma (aOR = 6.70, 95% CI: 3.59–12.50), and study period were independently associated with fungal positivity. Spring and autumn were associated with higher odds of FK than summer. Shannon diversity index increased from 1.03 pre-pandemic to 1.35 during the pandemic and 1.78 post-pandemic, indicating expanding species diversity. Aspergillus fumigatus (29.5%) and A. niger (27.2%) were the dominant isolates, while Penicillium spp., Alternaria spp., and less common fungi emerged more frequently in later phases. Temporal changes in the burden and mycological spectrum of FK were observed across the pandemic and post-pandemic phases, with the pandemic era being associated with a sustained increase in FK burden and broader species diversity. Ongoing laboratory-based surveillance and future prospective multicenter studies that integrate molecular and clinical outcome are warranted for a deeper comprehension of the factors driving these epidemiological patterns.