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Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India.

ABSTRACT: To evaluate the clinical utility of high-throughput sequencing (HTS) approach-based analysis of the bacterial and fungal genome in vitreous fluids from patients clinically diagnosed as endophthalmitis, we subjected 75 vitreous fluids from clinically presumed infectious endophthalmitis patients to high-throughput sequencing (Illumina HiSeq 2500) after DNA extraction and amplification of the 16S rRNA for the detection of bacteria, and ITS 2 region for detection of fungal pathogens. As controls, we included vitreous biopsies from 70 patients diagnosed with other non-infectious retinal disorders. Following the construction of the curated microbial genome database and filtering steps to reduce ambiguousness/contaminants from the environment, the paired reads were analyzed. Our HTS reads revealed in almost all cases the same organism that was grown in culture (bacterial-14/15, fungal 3/3) by conventional microbiological workup. HTS additionally diagnosed the presence of microbes in 42/57 (73.7%) patients who were conventionally negative (fungal pathogens in 36/57, bacterial pathogens in 11/57, including five cases that showed the presence of both bacterial and fungal organisms). Aspergillus sp., Fusarium sp., Exserohilum sp., and Candida sp. were the most predominant genera in our cohort of culture-negative endophthalmitis cases. Heat map based microbial clustering analysis revealed that these organisms were taxonomically similar to the species identified by conventional culture methods. Interestingly, 4/70 control samples also showed the presence of bacterial reads, although their clinical significance is uncertain. HTS is useful in detecting pathogens in endophthalmitis cases that elude conventional attempts at diagnosis and can provide actionable information relevant to management, especially where there is a high index of suspicion of fungal endophthalmitis, particularly in tropical countries. Outcome analyses and clinical trials addressing the success and cost savings of HTS for the diagnosis of endophthalmitis are recommended.

SUBMITTER: Gandhi J

PROVIDER: S-EPMC6843429 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India.

Gandhi Jaishree J Jayasudha Rajagopalaboopathi R Naik Poonam P Sharma Savitri S Dave Vivek Pravin VP Joseph Joveeta J

Microorganisms 20191001 10

To evaluate the clinical utility of high-throughput sequencing (HTS) approach-based analysis of the bacterial and fungal genome in vitreous fluids from patients clinically diagnosed as endophthalmitis, we subjected 75 vitreous fluids from clinically presumed infectious endophthalmitis patients to high-throughput sequencing (Illumina HiSeq 2500) after DNA extraction and amplification of the 16S rRNA for the detection of bacteria, and ITS 2 region for detection of fungal pathogens. As controls, we ...[more]

PMID: 31581465

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Project description:ImportanceFungal endophthalmitis caused by contaminated medical products is extremely rare; it follows an intractable clinical course with a poor visual prognosis.ObjectiveTo report the epidemiologic and clinical features and treatment outcomes of a nationwide fungal endophthalmitis outbreak after cataract surgery as a result of contaminated viscoelastic agents in South Korea.Design, setting, and participantsThis was a retrospective case series analysis of clinical data from multiple institutions in South Korea conducted from September 1, 2020, to October 31, 2021. Data were collected through nationwide surveys in May and October 2021 from the 100 members of the Korean Retinal Society. Patients were diagnosed with fungal endophthalmitis resulting from the use of the viscoelastic material sodium hyaluronate (Unial [Unimed Pharmaceutical Inc]). Data were analyzed from November 1, 2021, to May 30, 2022.Main outcomes and measuresThe clinical features and causative species were identified, and treatment outcomes were analyzed for patients who underwent 6 months of follow-up.ResultsThe fungal endophthalmitis outbreak developed between September 1, 2020, and June 30, 2021, and peaked in November 2020. An official investigation by the Korea Disease Control and Prevention Agency confirmed contamination of viscoelastic material. All 281 eyes of 265 patients (mean [SD] age, 65.4 [10.8] years; 153 female individuals [57.7%]) were diagnosed with fungal endophthalmitis, based on clinical examinations and supportive culture results. The mean (SD) time period between cataract surgery and diagnosis was 24.7 (17.3) days. Patients exhibited characteristic clinical features of fungal endophthalmitis, including vitreous opacity (212 of 281 [75.4%]), infiltration into the intraocular lens (143 of 281 [50.9%]), and ciliary infiltration (55 of 281 [19.6%]). Cultures were performed in 260 eyes, and fungal presence was confirmed in 103 eyes (39.6%). Among them, Fusarium species were identified in 89 eyes (86.4%). Among the 228 eyes included in the treatment outcome analysis, the mean (SD) best-corrected visual acuity improved from 0.78 (0.74) logMAR (Snellen equivalent, 20/120 [7.3 lines]) to 0.36 (0.49) logMAR (Snellen equivalent, 20/45 [4.9 lines]) at 6 months. Furthermore, disease remission with no signs of fungal endophthalmitis (or cells in the anterior chamber milder than grade 1) was noted in 214 eyes (93.9%).Conclusions and relevanceThis was a retrospectively reviewed case series of a fungal endophthalmitis outbreak resulting from contaminated viscoelastic material. Findings of this case series study support the potential benefit of prompt, aggressive surgical intervention that may reduce treatment burden and improve prognosis of fungal endophthalmitis caused by contaminated medical products.

Dataset Information

Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India.

Publications

Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India.

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