Metagenomic Next-Generation Sequencing Detects Pathogens in Endophthalmitis Patients

Abstract

Purpose: To investigate the utility of metagenomic next-generation sequencing (mNGS) in identifying the pathogens in endophthalmitis.Methods: In this prospective study, 36 cases of endophthalmitis were recruited. All patients received surgical treatment and intraocular drug lavage. The samples of vitreous or aqueous humor were extracted for mNGS and microbiological culture. The diagnostic performance of pathogens was compared between mNGS and culture.Results: The positive rates of mNGS and culture were 88.89% (32/36) and 27.78% (10/ 36), respectively. There was a statistically significant difference between mNGS and culture (Chi-square = 27.657; P , 0.01). Staphylococcus epidermidis, Streptococcus pneumoniae, and Klebsiella pneumoniae were the most pathogenic bacteria in traumatic, postoperative, and endogenous endophthalmitis, respectively. The concordance of pathogen identified by mNGS and culture was 70% for culture-positive cases. Antibiotic resistance genes were identified in 9 cases. There was a marginal correlation between the final visual acuity and the microbial sequence read (Spearman correlation coefficient = 0.498; P = 0.05).Conclusion: Metagenomic next-generation sequencing has a higher positive rate of identifying pathogens in endophthalmitis than in culture. It can also provide information on antibiotic resistance and visual prognosis. However, caution must be taken when interpreting the results of mNGS because they may not be concordant with culture.

Metagenomic Next-Generation Sequencing to Investigate Infectious Endophthalmitis of Brucella: A Case Report

“…For molecular detecting technology like qPCR technology and gene chips, a limited number of pathogens can be detected merely because specific primer sets are necessary ( 22 , 23 ). Compared to the methods above, mNGS is superior because it is an unbiased high-throughput sequencing approach that can theoretically detect all pathogens in a clinical sample in a short space of time ( 10 , 24 ). Furthermore, mNGS can provide antibiotic resistance information by comparing genes in the organisms with those in an antibiotic resistance database ( 9 , 24 , 25 ).…”

“…Compared to the methods above, mNGS is superior because it is an unbiased high-throughput sequencing approach that can theoretically detect all pathogens in a clinical sample in a short space of time ( 10 , 24 ). Furthermore, mNGS can provide antibiotic resistance information by comparing genes in the organisms with those in an antibiotic resistance database ( 9 , 24 , 25 ). In clinic, a small amount of extracted aqueous humor from puncture under slit lamp is sufficient for mNGS, which is a low-risk and convenient method compared to extracting the vitreous humor ( 26 ).…”

“…In clinic, a small amount of extracted aqueous humor from puncture under slit lamp is sufficient for mNGS, which is a low-risk and convenient method compared to extracting the vitreous humor ( 26 ). Hence, mNGS is a promising diagnostic tool for patients with difficult-to-diagnose endophthalmitis, and it provides information on antibiotic resistance and visual prognosis ( 24 , 27 ).…”

Application of High-Throughput Sequencing Technology in Identifying the Pathogens in Endophthalmitis

“…In one case, culture identified K. pneumoniae , but mNGS identified C. jeikeium and P. putida . The clinical manifestation and course were not consistent with K. pneumoniae endophthalmitis [ 18 ]. With the development of molecular biology and molecular genetics, particularly PCR, there has been a shift in the understanding of bacterial characteristics from structural to genetic material, and the detection of bacteria has also shifted to genetic-level detection.…”

“…Traditional cultures are often ineffective for slow-growing and rare micro-organisms, in which case HTS often has an advantage. Further, HTS may provide anti-biotic resistance information by comparing genes in an organism with genes in the anti-biotic resistance database, rather than relying solely on empirical administration [ 18 , 43 ].…”