IDENTIFICATION OF PATHOGENS IN THE INTRAOCULAR FLUID SAMPLES OF PATIENTS WITH ENDOGENOUS ENDOPHTHALMITIS USING RAPID NANOPORE TARGETED SEQUENCING.

IN BRIEF: Nanopore targeted sequencing showed a higher positivity rate and a shorter turnaround time than did traditional culture in identifying pathogens in the intraocular fluid samples of patients with endogenous endophthalmitis. PURPOSE: To evaluate the feasibility of clinical application of nanopore targeted sequencing (NTS) for the identification of pathogens in patients with endogenous endophthalmitis, especially those with fungus-associated endophthalmitis. METHODS: In this retrospective study, medical records and etiological results of 27 patients (34 eyes) with endogenous endophthalmitis were reviewed. The intraocular fluid samples were examined using both NTS and microbial culture. The results included the differences in detection time, positivity rate of pathogen detection, and positivity rate of fungus identification between two methods. RESULTS: NTS and microbial culture enabled the detection of etiologic agents in 89.28% and 35.71% of the samples, respectively. The difference of positivity rate between these methods was statistically significant ( P < 0.001). NTS also showed high sensitivity in both culture-positive and culture-negative samples (100% and 83.33%, respectively). Regarding culture-positive samples, the NTS results displayed a strong match with culture results. NTS showed a significantly higher positivity rate for fungal infection than did microbial culture (46.43% vs. 7.14%, P = 0.002). The average detection time of NTS was 1.11 ± 0.31 days, which was shorter than that of microbial culture (2.50 ± 0.58 days, Z = -4.686, P < 0.001). NTS technology facilitated an informed switch of intravitreal antimicrobial agents in 13 eyes. CONCLUSION: NTS, as a sensitive, specific, and timely complementary method, can be used along with traditional methods for the identification of pathogenic microorganisms in the intraocular fluid of patients with endogenous endophthalmitis.