Background Microorganism identification is critical for the early diagnosis and management of infectious endophthalmitis, but traditional culture can yield false‐negative results. Nanopore targeted sequencing (NTS) is a third‐generation sequencing technique with multiple advantages. This study aimed to test aqueous humour or vitreous fluid samples from presumed cases of infectious endophthalmitis using NTS to evaluate the feasibility of NTS in diagnosing endophthalmitis, especially for culture‐negative cases. Methods This prospective study enrolled patients who presented to the Department of Ophthalmology of Union Hospital (Wuhan, China) between June 2018 and December 2020. The samples were sent immediately for routine microbiology culture processing and NTS assay. Results NTS identified microorganisms in 17 of 18 cases (94.4%) (eight culture‐positive cases, nine culture‐negative cases, and one case unavailable for culture). There was a high‐quality match between culture and NTS for culture‐positive cases. In the eight culture‐negative cases and the case unavailable for culture, NTS detected either bacteria, fungi, or a mixture of bacteria and fungi in the intraocular fluids. The average waiting times for the results of bacterial and fungal cultures were 48 and 72 h, respectively. The average time for the NTS results was 12 h. Conclusions NTS appears to be a promising diagnostic platform for diagnosing infectious endophthalmitis, even for culture‐negative cases.

Endophthalmitis is a rare and infectious disease caused by Streptococcus suis (S suis). Traditionally, S suis is detected by the pathogenic microorganism culture method, which has low positivity and high false negativity. Nanopore sequencing (NS), which is a third-generation sequencing technology, has several advantages over the traditional method; in particular, it is cost and time effective and has a high throughput. In this report, a case of infectious endophthalmitis caused by trauma is examined. The NS results suggest that the pathogen in question is a mixed infection caused by S suis and Clostridium perfringens. This case report provides evidence of the fact that NS can quickly identify pathogens, which is of great significance for clinical diagnosis and treatment.

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