Prognostic Utility of Whole-Genome Sequencing and Polymerase Chain Reaction Tests of Ocular Fluids in Postprocedural Endophthalmitis

Lee, Cecilia S.; Hong, Bryan; Kasi, Sundeep; Aderman, Christopher M.; Talcott, Katherine E.; Adam, Murtaza K.; Yue, Bryan; Akileswaran, Lakshmi; Nakamichi, Kenji; Wu, Yue; Rezaei, Kasra A.; Koo, Lisa C. Olmos de; Chee, Yewlin E.; Lee, Aaron; Gelder, Russell N. Van

doi:10.1016/j.ajo.2020.03.008

Cited by 19 publications

(27 citation statements)

References 35 publications

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“…In our study, there were no observable differences in the identification of microbial sequences between aqueous or vitreous fluid biopsy samples using nanopore sequencing, which is in concordance to the previously published studies using Illumina sequencing 10,17,19 .…”

Section: Definitionssupporting

confidence: 92%

“…The organism was known to be potentially pathogenic given the clinical context of the particular patient 17 2. The organism represented the highest bacterial load (for WGS) or most abundant reads (for 16S) in the sample 17,33 Bacterial load was defined as the median number of the presumed pathogen per recovered human genome by whole genome sequencing 10 nanopore, Nanopore WGS and Illumina WGS were 75%, 100% and 78% respectively. Taken together, these results suggest that nanopore sequencing may provide useful information on the pathogens associated with endophthalmitis.…”

Section: Definitionsmentioning

confidence: 99%

“…Molecular sequencing technology has the potential in advancing diagnostics for ocular infections 10,[17][18][19]40 . Using metagenomic deep sequencing, Doan and associates were able to detect the presence of RV virus (Rubivirus genus) in the intraocular fluid sample of a patient with a 16-year history of idiopathic uveitis.…”

Section: Definitionsmentioning

confidence: 99%

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Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform

Low¹,

Nakamichi²,

Akileswaran³

et al. 2022

American Journal of Ophthalmology

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Section: Definitionssupporting

confidence: 92%

Section: Definitionsmentioning

confidence: 99%

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Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform

Low¹,

Nakamichi²,

Akileswaran³

et al. 2022

American Journal of Ophthalmology

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“…It was reported that the presence and higher load of bacteria other than S. epidermidis were associated with worse outcomes in postprocedure endophthalmitis. 42 We also found a marginal correlation between the final visual acuity and the microbial sequence read (rs = 0.498; P = 0.050). It suggests that the mNGS data can also be used to predict the prognosis of endophthalmitis.…”

Section: Discussionmentioning

confidence: 61%

Metagenomic Next-Generation Sequencing Detects Pathogens in Endophthalmitis Patients

Zhu

Tang

et al. 2022

Retina

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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.

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“…Among the remaining samples, one case showed that the culture result was Staphylococcus aureus , and the WGS result showed that Pseudomonas was the dominant strain. These results suggest that there may be deviations in the identification of the primary endophthalmitis-causing pathogens [ 36 ]. Compared with first-generation sequencing technology, second-generation sequencing technology has a longer read length and higher throughput; however, the outstanding features of third-generation sequencing technology are single-molecule sequencing and long read length [ 41 ].…”

Section: The Application Of Hts In the Study Of Endophthalmitis Floramentioning

confidence: 99%

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

Cheng

Dong

Kang

et al. 2022

Journal of Ophthalmology

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Infectious endophthalmitis is an important cause of vision loss worldwide. It is an inflammatory reaction caused by bacteria, fungi, and other micro-organisms and often occurs as a complication of intraocular surgery, especially following cataract surgery or intravitreal injection. The focus of the prevention and treatment of infectious endophthalmitis is the early detection of microbial flora, such as fungi or bacteria. Current identification methods for bacteria include Gram staining-based, culture-based, and polymerase chain reaction (PCR)-based methods. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technology is now the standard identification method of bacteria and fungi after their isolation in culture. The remarkable sensitivity of PCR technology for the direct detection of micro-organisms in clinical samples makes it particularly useful in culture-positive and culture-negative endophthalmitis. Furthermore, PCR increases the rate of microorganism detection in intraocular samples by 20% and can provide a microbiology diagnosis in approximately 44.7–100% of the culture-negative cases. This review aims to introduce the development of different methods for the detection and identification of micro-organisms causing endophthalmitis through a literature review; introduce the research status of the first, second, and third-generation sequencing technologies in infectious endophthalmitis; and understand the research status of endophthalmitis microbial flora. For slow-growing and rare micro-organisms, high-throughput sequencing (HTS) offers advantages over conventional methods and provides a basis for the identification of pathogens in endophthalmitis cases with negative culture. It is a reliable platform for the identification of pathogenic bacteria of infectious endophthalmitis in the future and provides a reference for the clinical diagnosis and treatment of infectious endophthalmitis. The application of HTS technology may also be transformative for clinical microbiology and represents an exciting future direction for the epidemiology of ocular infections.

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Prognostic Utility of Whole-Genome Sequencing and Polymerase Chain Reaction Tests of Ocular Fluids in Postprocedural Endophthalmitis

Cited by 19 publications

References 35 publications

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform

Metagenomic Next-Generation Sequencing Detects Pathogens in Endophthalmitis Patients

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

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