Pathogen-oriented targeted next-generation sequencing as an adjunctive tool for detection of pathogens in...

Endophthalmitis represents one of the most severe ophthalmic emergencies, requiring prompt etiological identification to enable tailored antibiotic administration. Conventional identification methods, such as ocular sample culture, exhibit limited positivity in endophthalmitis, necessitating more advanced approaches.

The performance of pathogen-oriented targeted next-generation sequencing (tNGS), designed to capture a predefined panel of 207 clinically relevant pathogens, was retrospectively evaluated in 43 patients with endophthalmitis.

The positivity rate of culture was 22.2% (8/36, 95% CI: 10.1-39.2%), whereas that of tNGS was 86.0% (37/43, 95% CI, 72.1-94.7%). tNGS had a turnaround time of less than 24 h, facilitated the detection of polymicrobial infection, and identified microbes in 91.7% (11/12) of specimens that were negative for both smear and culture. Among the 36 paired specimens subjected to both culture and tNGS, tNGS achieved microbial identification in 25 of 28 culture-negative specimens (89.3%), and its positivity rate (88.9%, 32/36, 95% CI, 73.9-96.9%) was significantly higher than that of culture (p < 0.001), with the difference being 66.7% (95% CI, 44.4-80.6%). Poor agreement between tNGS and culture was observed (Kappa = -0.009, p = 0.887). The positivity rate of tNGS was 100% (9/9) for aqueous humour specimens, and 85.2% (23/27) for vitreous specimens. Additionally, there was no statistically significant difference in the positivity rate of tNGS among endogenous, post-traumatic, and post-operative endophthalmitis (p = 0.666). The application of tNGS impacted therapeutic strategy selection and contributed to the control of infections in cases caused by uncommon pathogens (e.g., mycobacterial infection), in endogenous endophthalmitis, and particularly in fungal endophthalmitis.

The higher positivity and shorter turnaround time of pathogen-oriented tNGS render it an adjunctive tool for enhancing pathogen identification in endophthalmitis. We recommend the routine application of tNGS as a valuable complement to culture, in order to facilitate and expedite pathogen detection, thereby advancing efforts toward tailored precision medicine in the management of endophthalmitis.