@article {1596, title = {Comparison of antimicrobial resistance genes on the ocular surface of patients with corneal infections in California and Malawi.}, journal = {Int Health}, year = {2025}, month = {2025 Apr 29}, abstract = {

BACKGROUND: Antimicrobial resistance (AMR) determinants on the ocular surface may contribute to poor treatment responses.

METHODS: An exploratory comparative analysis of ocular surface AMR determinants, as determined by RNA-sequencing (RNA-seq), on patients presenting with corneal infections at the Proctor Medical Clinic at the University of California San Francisco in San Francisco, CA, USA, and the Queen Elizabeth Central Hospital at the Department of Ophthalmology of Kamuzu College of Health Sciences in Blantyre, Malawi, was conducted. All patients underwent swabbing of three sites on the ocular surface: cornea, ipsilateral conjunctiva, and contralateral conjunctiva.

RESULTS: Mutations conferring macrolide resistance were present on the ocular surface in 58\% (95\% CI 44 to 71\%) of the participants in Malawi and 32\% (95\% CI 20 to 46\%) of the participants in San Francisco. Aminoglycosides resistance genes were also common on the ocular surface with 58\% (95\% CI 44 to 71\%) prevalence in Malawi and 21\% (95\% CI 12 to 35\%) in San Francisco. AMR was associated with poorer visual outcomes in a subset of patients.

CONCLUSIONS: As determined by RNA-seq, ocular surface AMR gene mutations are common in patients with infectious keratitis. Surveillance may be important for infectious keratitis treatment selection as well as providing guidance for antibiotic stewardship.

}, issn = {1876-3405}, doi = {10.1093/inthealth/ihaf042}, author = {Seitzman, Gerami D and Kalua, Khumbo and Misanjo, Esther S and Chen, Cindi and Ouimette, Kevin and Zhong, Lina and Liu, YuHeng and Yu, Danny and Abraham, Thomas and Wu, Nathaniel and Yan, Daisy and Lietman, Thomas M and Hinterwirth, Armin and Doan, Thuy} } @article {1611, title = {Epstein-Barr Virus Associated with Unilateral Thygeson{\textquoteright}s Superficial Punctate Keratitis.}, journal = {Ophthalmology}, year = {2025}, month = {2025 May 31}, issn = {1549-4713}, doi = {10.1016/j.ophtha.2025.04.029}, author = {Nesemann, John M and Doan, Thuy and Seitzman, Gerami D} } @article {1456, title = {Association of weather variables with pathogens contributing to conjunctivitis worldwide.}, journal = {Clin Infect Dis}, year = {2024}, month = {2024 Aug 19}, abstract = {

PURPOSE: To identify weather variables associated with pathogens contributing to infectious conjunctivitis globally.

METHODS: Sample collection and pathogen identification from patients with acute infectious conjunctivitis was performed from 2017 to 2023. We linked pathogens identified from 13 sites across 8 countries with publicly available weather data by geographic coordinates. Mixed effects logistic regression analysis was performed to estimate the associations between temperature, precipitation, and relative humidity exposures, and the prevalence of infection types (RNA virus, DNA virus, bacteria, and fungus).

RESULTS: 498 cases from the United States, India, Nepal, Thailand, Burkina Faso, Niger, Vietnam, and Israel were included in the analysis. 8-day average precipitation (mm) was associated with increased odds of RNA virus infection (odds ratio (OR)=1.47, 95\% confidence interval (CI): 1.12 to 1.93, P=0.01) and decreased odds of DNA infection (OR=0.62, 95\% CI: 0.46 to 0.82, P\<0.001). Relative humidity (\%) was associated with increased odds of RNA virus infections (OR=2.64, 95\% CI: 1.51 to 4.61, P\<0.001), and fungal infections (OR=2.35, 95\% CI: 1.19 to 4.66, P=0.01), but decreased odds of DNA virus (OR=0.58, 95\%CI: 0.37 to 0.90, P=0.02) and bacterial infections (OR=0.42, 95\% CI: 0.25 to 0.71, P\<0.001). Temperature ({\textdegree}C) was not associated with ocular infections for any pathogen type.

CONCLUSIONS: This study suggests that weather factors affect pathogens differently. Particularly, humidity and precipitation were predictors for pathogens contributing to conjunctivitis worldwide. Additional work is needed to clarify the effects of shifts in weather and environmental factors on ocular infectious diseases.

}, issn = {1537-6591}, doi = {10.1093/cid/ciae417}, author = {Yan, Daisy and Prajna, N Venkatesh and Lalitha, Prajna and Sansanayudh, Wiwan and Satitpitakul, Vannarut and Laovirojjanakul, Wipada and Chaudhary, Meenu and Bountogo, Mamadou and Sie, Ali and Coulibaly, Boubacar and Amza, Abdou and Nassirou, Beido and Almou, Ibrahim and Tran, Huy and Tran, Yen and Tsui, Edmund and Onclinx, Tania and Sella, Ruti and Goren, Lee and McClean, Esmeralda and Tham, Vivien and Chen, Cindi and Ruder, Kevin and Zhong, Lina and Liu, YuHeng and Yu, Danny and Abraham, Thomas and Lebas, Elodie and Arnold, Benjamin F and McLeod, Stephen D and Deiner, Michael S and Porco, Travis C and Seitzman, Gerami D and Lietman, Thomas M and Shantha, Jessica and Hinterwirth, Armin and Doan, Thuy} } @article {1451, title = {Biomarker Detection and Validation for Corneal Involvement in Patients With Acute Infectious Conjunctivitis.}, journal = {JAMA Ophthalmol}, year = {2024}, month = {2024 Aug 15}, abstract = {

IMPORTANCE: Infectious conjunctivitis can lead to corneal involvement and result in ocular morbidity. The identification of biomarkers associated with corneal involvement has the potential to improve patient care.

OBJECTIVE: To identify biomarkers in patients with acute infectious conjunctivitis.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study took place from December 2016 to March 2024. Analyses were performed in 3 phases. First, logistic regression and machine learning algorithms were used to predict the probability of demonstrating corneal involvement in patients with presumed infectious conjunctivitis. Second, quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to confirm the most important biomarker gene identified by the algorithm. Third, the biomarker gene was validated in prospectively collected conjunctival samples of adult patients from 3 outpatient centers in Thailand and 1 in India. Patients with signs and symptoms of infectious conjunctivitis and onset within less than 14 days were eligible. Exclusion criteria were the inability to consent, presumed toxicity, or allergic conjunctivitis.

EXPOSURES: Acute infectious conjunctivitis.

MAIN OUTCOMES AND MEASURES: The identification and validation of ocular surface gene expression associated with corneal findings on slitlamp examination.

RESULTS: Thirteen genes exhibited a 1.5-log2 fold change in expression in patients with corneal involvement compared to patients without corneal involvement. Using the 13 genes to train and cross validate, logistic regression produced the highest mean area under the receiver operating characteristic curve (AUROC; 0.85; 95\% CI, 0.84-0.86) for corneal involvement. The removal of apolipoprotein E (APOE) from the gene ensemble led to a decline in predictive performance of the logistic regression classifier (from mean AUROC 0.85 [95\% CI, 0.84-0.86] to 0.74 [95\% CI, 0.73-0.75]; adjusted P = .001 [Tukey test]). Orthogonal testing of APOE expression level with RT-qPCR showed that APOE expression was higher in patients with corneal involvement compared to patients without (median [IQR], 0.23 [0.04-0.47] vs 0.04 [0.02-0.06]; P = .004 [Mann-Whitney U test]). Using a Youden index of 0.23 Δ threshold cycle, APOE had a sensitivity of 56\% (95\% CI, 33-77) and a specificity of 88\% (95\% CI, 79-93) in 106 samples with conjunctivitis at Aravind, India (P < .001 [Fisher exact test]). When applied to a different patient population in Thailand, the same criteria could discriminate between disease states (58 samples; sensitivity, 47\%; 95\% CI, 30-64 and specificity, 93\%; 95\% CI, 77-99; P = .001 [Fisher exact test]).

CONCLUSIONS AND RELEVANCE: The results from this study suggest that the host conjunctival immune response can be meaningfully interrogated to identify biomarkers for ocular surface diseases.

}, issn = {2168-6173}, doi = {10.1001/jamaophthalmol.2024.2891}, author = {Seitzman, Gerami D and Prajna, Lalitha and Prajna, N Venkatesh and Sansanayudh, Wiwan and Satitpitakul, Vannarut and Laovirojjanakul, Wipada and Chen, Cindi and Zhong, Lina and Ouimette, Kevin and Redd, Travis and Deiner, Michael C and Porco, Travis C and McLeod, Stephen D and Lietman, Thomas M and Hinterwirth, Armin and Doan, Thuy} } @article {1416, title = {Coxsackievirus A24 Causing Acute Conjunctivitis in a 2023 outbreak in Vietnam.}, journal = {Int J Infect Dis}, year = {2024}, month = {2024 Jun 12}, pages = {107133}, abstract = {

OBJECTIVES: To determine the causative pathogen during the 2023 conjunctivitis outbreak in Vietnam METHODS: RNA-sequencing was used to identify pathogens before and during the outbreak.

RESULTS: 24 patients with infectious conjunctivitis between March and October 2023 from Hai Yen Vision Institute in Vietnam were swabbed. Coxsackievirus A24v was the most common pathogen identified. Phylogenetic analysis of these strains demonstrates similarities to the Coxsackievirus identified in the 2022 India outbreak. Human adenovirus D was also circulating. Ocular findings of tearing, purulence, and itching were common in this outbreak.

CONCLUSIONS: Multiple viruses can co-circulate during conjunctivitis outbreaks. Hemorrhagic conjunctivitis, commonly associated with coxsackievirus conjunctivitis, was not a common clinical sign in this outbreak. Repeat genetic surveillance, with the notable inclusion of RNA virus detection strategies, is important for outbreak detection.

}, issn = {1878-3511}, doi = {10.1016/j.ijid.2024.107133}, author = {Tran, Huy and Hạ, Thảo and Hoang, Linh and Tran, Yen and Ruder, Kevin and Zhong, Lina and Chen, Cindi and Liu, YuHeng and Yu, Danny and Abraham, Thomas and Hinterwirth, Armin and Deiner, Michael and Porco, Travis C and Lietman, Thomas M and Doan, Thuy and Seitzman, Gerami D} } @article {1436, title = {Etiologies of Infectious Keratitis in Malawi.}, journal = {Am J Trop Med Hyg}, year = {2024}, month = {2024 Jul 16}, abstract = {

Infectious keratitis is a leading cause of corneal blindness worldwide with little information known about causative etiologies in Malawi, Africa. This area is resource-limited with ophthalmologist and microbiology services. The Department of Ophthalmology at the Kamuzu College of Health Sciences in Blantyre, Malawi, is a participating site of an international corneal ulcer consortium, capriCORN (Comprehensive Analysis of Pathogens, Resistomes, and Inflammatory-markers in the CORNea). In this study, 50 patients with corneal ulcers were swabbed for pathogen identification using RNA-sequencing. Corneal trauma was reported in 41\% and 19\% of the patients worked in agriculture. A pathogen was identified in 58\% of the cases. Fungal pathogens predominated, followed by viruses and bacteria. Aspergillus, Fusarium, HSV-1, and Gardnerella were the most common pathogens detected. 50\% of patients reported treatment with an antibiotic before presentation. Pathogens unusual for infectious keratitis, such as Subramaniula asteroids, Aureobasidium pullulans, and Gardnerella vaginalis, were also detected.

}, issn = {1476-1645}, doi = {10.4269/ajtmh.24-0149}, author = {Kalua, Khumbo and Misanjo, Esther S and Lietman, Thomas M and Ruder, Kevin and Zhong, Lina and Chen, Cindi and Liu, YuHeng and Yu, Danny and Abraham, Thomas and Wu, Nathaniel and Yan, Daisy and Hinterwirth, Armin and Doan, Thuy and Seitzman, Gerami D} } @article {1396, title = {Human Conjunctival Transcriptome in Acanthamoeba Keratitis: An Exploratory Study.}, journal = {Cornea}, year = {2024}, month = {2024 May 21}, abstract = {

PURPOSE: The purpose of this study was to identify conjunctival transcriptome differences in patients with Acanthamoeba keratitis compared with keratitis with no known associated pathogen.

METHODS: The host conjunctival transcriptome of 9 patients with Acanthamoeba keratitis (AK) is compared with the host conjunctival transcriptome of 13 patients with pathogen-free keratitis. Culture and/or confocal confirmed Acanthamoeba in 8 of 9 participants with AK who underwent metagenomic RNA sequencing as the likely pathogen. Cultures were negative in all 13 cases where metagenomic RNA sequencing did not identify a pathogen.

RESULTS: Transcriptome analysis identified 36 genes differently expressed between patients with AK and patients with presumed sterile, or pathogen-free, keratitis. Gene enrichment analysis revealed that some of these genes participate in several biologic pathways important for cellular signaling, ion transport and homeostasis, glucose transport, and mitochondrial metabolism. Notable relatively differentially expressed genes with potential relevance to Acanthamoeba infection included CPS1, SLC35B4, STEAP2, ATP2B2, NMNAT3, and AKAP12.

CONCLUSIONS: This research suggests that the local transcriptome in Acanthamoeba keratitis may be sufficiently robust to be detected in the conjunctiva and that corneas infected with Acanthamoeba may be distinguished from the inflamed cornea where no pathogen was identified. Given the low sensitivity for corneal cultures, identification of differentially expressed genes may serve as a suggestive transcriptional signature allowing for a complementary diagnostic technique to identify this blinding parasite. Knowledge of differentially expressed genes may also direct investigation of disease pathophysiology and suggest novel pathways for therapeutic targets.

}, issn = {1536-4798}, doi = {10.1097/ICO.0000000000003545}, author = {Seitzman, Gerami D and Keenan, Jeremy D and Lietman, Thomas M and Ruder, Kevin and Zhong, Lina and Chen, Cindi and Liu, YuHeng and Yu, Danny and Abraham, Thomas and Hinterwirth, Armin and Doan, Thuy} } @article {1406, title = {Ocular manifestations of mpox.}, journal = {Curr Opin Ophthalmol}, year = {2024}, month = {2024 Jun 07}, abstract = {

PURPOSE OF REVIEW: To highlight the clinical features of mpox with an emphasis on ocular manifestations and to review treatment options for this re-emerging infectious disease.

RECENT FINDINGS: Ocular involvement of mpox varies by clade. The most recent 2022 outbreak appears to be associated with fewer conjunctivitis cases compared to previous outbreaks. However, the ocular findings occurring during this newly emerging clade can be visually threatening and include cases of keratitis, rapidly progressing scleritis, and necrotizing periorbital rashes.

SUMMARY: Ocular mpox is an important clinical feature of systemic mpox virus (MPXV) infection. Heightened clinical suspicion allows for a timely diagnosis and the initiation of antiviral treatment, when appropriate. Randomized clinical trials for mpox systemic and ocular treatment efficacy are lacking. Prior clinical experience with smallpox and in-vitro mpox data support the use of systemic antivirals such as tecovirimat, cidofovir, brincidofovir and topical use of trifluridine in ocular mpox management, though treatment-resistant infection can occur and portend a poor prognosis.

}, issn = {1531-7021}, doi = {10.1097/ICU.0000000000001066}, author = {Nguyen, Minh and Doan, Thuy and Seitzman, Gerami D} } @article {1191, title = {Case Series: Unbiased Deep Sequencing Analysis of Acute Infectious Conjunctivitis in an Ambulatory Eye Center in Berkeley, California.}, journal = {Optom Vis Sci}, year = {2023}, month = {2023 Mar 07}, abstract = {

SIGNIFICANCE: Acute infectious conjunctivitis poses significant challenges to eye care providers. It can be highly transmissible and as etiology is often presumed, correct treatment and management can be difficult. This study utilizes unbiased deep sequencing to identify causative pathogens of infectious conjunctivitis, potentially allowing for improved approaches to diagnosis and management.

PURPOSES: To identified associated pathogens of acute infectious conjunctivitis in a single ambulatory eye care center.Case ReportsThis study included patients who presented to the University of California Berkeley eye center with signs and symptoms suggestive of infectious conjunctivitis. From December 2021 to July 2021, samples were collected from 7 subjects (ages ranging from 18 to 38 years old). Deep sequencing identified associated pathogens in 5 out of 7 samples, including human adenovirus D (HAdV), Haemophilus influenzae, Chlamydia trachomatis, and human coronavirus 229E (HCoV-229E).

CONCLUSIONS: Unbiased deep sequencing identified some unexpected pathogens in subjects with acute infectious conjunctivitis. HAdV was recovered from only one patient in this series. While all samples were obtained during the COVID-19 pandemic, only one case of HCoV-229E and no SARS-CoV-2was identified.

}, issn = {1538-9235}, doi = {10.1097/OPX.0000000000002010}, author = {Kanai, Kuniyoshi and Whiteside, Meredith and Wong, Michel and La, Tammy and Nassiri, Maryam and Lee, Sam and Yeung, Sze Kei and Coulter, Adrienne and Ruder, Kevin and Chen, Cindi and Liu, David and Abraham, Thomas and Hinterwirth, Armin and Lietmanb, Thomas M and Doan, Thuy and Seitzman, Gerami D} } @article {1351, title = {Comprehensive Profile of Pathogens and Antimicrobial Resistance in Conjunctivitis Cases from Niger.}, journal = {Am J Trop Med Hyg}, volume = {109}, year = {2023}, month = {2023 Dec 06}, pages = {1333-1338}, abstract = {

Infectious conjunctivitis outbreaks remain a public health burden. This study focuses on the pathogen and antimicrobial resistance (AMR) profiles identified in Niger. Sixty-two patients with acute infectious conjunctivitis who presented to health posts were enrolled from December 2021 to May 2022. Nasal and conjunctival swabs were obtained from each patient. Unbiased RNA deep sequencing (RNA-seq) was used to identify associated pathogens. A pathogen was identified in 39 patients (63\%; 95\% CI, 50-74). Of those, an RNA virus was detected in 23 patients (59\%; 95\% CI, 43-73). RNA viruses were diverse and included human coronaviruses (HCoVs): SARS-CoV-2, HCoV-229E, HCoV-HKU1, and HCoV-OC43. A DNA virus was identified in 11 patients (28\%; 95\% CI, 17-44). Of those, four patients had a coinfection with an RNA virus and two patients had a coinfection with both an RNA virus and a bacterium. DNA viruses were predominantly human herpesvirus (cytomegalovirus, Epstein-Barr virus, human herpesvirus 8) and human adenovirus species B, C, and F. Eighteen patients (46\%; 95\% CI, 32-61) had a bacteria-associated infection that included Haemophilus influenza, Haemophilus aegyptius, Staphylococcus aureus, Streptococcus pneumoniae, and Moraxella spp. Antimicrobial resistance determinants were detected in either the conjunctiva or nasal samples of 20 patients (32\%; 95\% CI, 22-45) and were found to be more diverse in the nose (Shannon alpha diversity, 1.12 [95\% CI, 1.05-1.26] versus 1.02 [95\% CI, 1.00-1.05], P = 0.01). These results suggest the potential utility of leveraging RNA-seq to surveil pathogens and AMR for ocular infections.

}, issn = {1476-1645}, doi = {10.4269/ajtmh.23-0498}, author = {Amza, Abdou and Nassirou, Beido and Kadri, Boubacar and Ali, Saley and Mariama, Boubacar and Ibrahim, Ciss{\'e} Mamadou and Roufaye, Lamine Aboubacar and Lebas, Elodie and Colby, Emily and Zhong, Lina and Chen, Cindi and Ruder, Kevin and Yu, Danny and Liu, YuHeng and Abraham, Thomas and Chang, Aaron and Mai, Lina and Hinterwirth, Armin and Seitzman, Gerami D and Lietman, Thomas M and Doan, Thuy} } @article {1221, title = {Isolated Ocular Mpox without Skin Lesions, United States.}, journal = {Emerg Infect Dis}, volume = {29}, year = {2023}, month = {2023 Jun}, pages = {1285-1288}, abstract = {

We report a case of a 53-year-old HIV-negative patient in San Francisco, California, USA, with no classic mpox prodromal symptoms or skin lesions who experienced fulminant, vision-threatening scleritis, keratitis, and uveitis. Deep sequence analysis identified monkeypox virus RNA in the aqueous humor. We confirmed the virus on the cornea and sclera by PCR.

}, keywords = {Face, Humans, Middle Aged, Monkeypox, Polymerase Chain Reaction, Prodromal Symptoms, RNA, Viral, United States}, issn = {1080-6059}, doi = {10.3201/eid2906.230032}, author = {Nguyen, Minh T and Mentreddy, Akshay and Schallhorn, Julie and Chan, Matilda and Aung, Su and Doernberg, Sarah B and Babik, Jennifer and Miles, Kevin and Yang, Katherine and Lydon, Emily and Minter, Daniel J and Gonzales, John and Shantha, Jessica and Doan, Thuy and Seitzman, Gerami D} } @article {1411, title = {Pathogen Profiles of Infectious Conjunctivitis in Ho Chi Minh City, Vietnam.}, journal = {Cornea Open}, volume = {2}, year = {2023}, month = {2023 Dec}, abstract = {

PURPOSE: Conjunctivitis epidemics and pandemics remain a global burden. This study aims to comprehensively identify pathogens associated with conjunctivitis in Vietnam.

METHODS: Patients with acute conjunctivitis presented to an outpatient clinic in Ho Chi Minh City, Vietnam, were enrolled from September 2022 to March 2023. Swabs were obtained from conjunctiva and anterior nares of all patients. Unbiased RNA deep sequencing (RNA-seq) was used to identify any replicating pathogens in the samples.

RESULTS: Samples from 35 patients were analyzed. A pathogen was identified in 80\% of the patients. 72\% (95\% confidence interval: 54\% to 85\%) were infected with either HAdV-D or HAdV-B. RNA viruses detected were rhinoviruses and human coronavirus 229E. Bacteria etiologies included , , and One patient had co-infection of rhinovirus A and HAdV-B. , a fungus, was identified in one patient. Corneal sub-epithelial infiltrates, pseudomembranes, or pre-auricular lymphadenopathy were not reported in any patient.

CONCLUSIONS: Human adenoviruses are the common circulating pathogens associated with infectious conjunctivitis in Vietnam. HAdV species, however, appear to vary between geographic locations within Vietnam. Other under-recognized pathogens identified in this study, such as RNA viruses, suggest broader pathogen surveillance may be beneficial.

}, issn = {2833-6992}, doi = {10.1097/coa.0000000000000025}, author = {Tran, Huy and Hoang, Linh and Tran, Yen and Hạ, Thảo and Ruder, Kevin and Zhong, Lina and Chen, Cindi and Yu, Danny and Liu, YuHeng and Abraham, Thomas and Hinterwirth, Armin and Deiner, Michael and Porco, Travis and Lietman, Thomas M and Seitzman, Gerami D and Doan, Thuy} } @article {1356, title = {Pathogen Surveillance for Acute Infectious Conjunctivitis.}, journal = {JAMA Ophthalmol}, year = {2023}, month = {2023 Nov 02}, abstract = {

IMPORTANCE: Acute infectious conjunctivitis is a common ocular condition with major public health consequences.

OBJECTIVE: To assess regional variations and microbial etiologies of acute infectious conjunctivitis to guide treatment.

DESIGN, SETTING, AND PARTICIPANTS: In this cross-sectional study, patients with presumed acute infectious conjunctivitis were enrolled in the study at 5 sites (Honolulu, Hawaii; Los Angeles, San Francisco, and San Diego, California; and Petah-Tikva, Israel) from March 2021 to March 2023. Patients with allergic or toxic conjunctivitis were excluded.

MAIN OUTCOMES AND MEASURES: Pathogens were identified by unbiased RNA deep sequencing.

RESULTS: In all, 52 patients (mean [range] age, 48 [7-80] years; 31 females [60\%]) were enrolled at 5 sites (6 patients from Honolulu, 9 from San Diego, 11 from Los Angeles, 13 from San Francisco, and 13 from Petah-Tikva). RNA deep sequencing detected human adenovirus species D in one-quarter of patients (13 of 52). A wide range of pathogens, including human coronavirus 229E, SARS-CoV-2, and herpes simplex virus type 1, was also identified, as well as several bacteria and fungi. Moreover, 62\% (32 of 52) of patients presented with purulent discharge, while only 8\% (4 of 52) of patients had confirmed bacterial pathogens.

CONCLUSION AND RELEVANCE: In this cross-sectional study, pathogens associated with acute infectious conjunctivitis varied between all 5 sites in the US and Israel. Purulent discharge was a common presenting sign in this study, with a low specificity for bacteria-associated conjunctivitis, suggesting that further diagnostic workup may be necessary to inform antibiotic stewardship. Additional research on cost-effectiveness of using RNA deep sequencing is needed to ascertain whether it is better to monitor patients clinically until resolution of disease.

}, issn = {2168-6173}, doi = {10.1001/jamaophthalmol.2023.4785}, author = {Tsui, Edmund and Sella, Ruti and Tham, Vivien and Kong, Alan W and McClean, Esmeralda and Goren, Lee and Bahar, Irit and Cherian, Nina and Ramirez, Joana and Hughes, Reginald E and Privratsky, Joseph K and Onclinx, Tania and Feit-Leichman, Rachel and Cheng, Angel and Molina, Iliana and Kim, Phillip and Yu, Carol and Ruder, Kevin and Tan, Alexander and Chen, Cindi and Liu, YuHeng and Abraham, Thomas and Hinterwirth, Armin and Zhong, Lina and Porco, Travis C and Lietman, Thomas M and Seitzman, Gerami D and Doan, Thuy} } @article {891, title = {Deep sequencing analysis of acute conjunctivitis in Burkina Faso, Africa.}, journal = {Int Health}, year = {2022}, month = {2022 Jan 24}, abstract = {

BACKGROUND: Seasonal and epidemic conjunctivitis (pink eye) infections are highly contagious and impose a significant economic burden worldwide. Long-term visual impairment can occur.

METHODS: This study used metagenomic deep sequencing to evaluate pathogens causing acute infectious conjunctivitis in Burkina Faso.

RESULTS: We found that pathogens causing conjunctivitis in Burkina Faso are diverse, with human adenoviruses responsible for a small fraction of the samples tested.

CONCLUSIONS: These results are unexpected and suggest the importance of regional surveillance.

}, issn = {1876-3405}, doi = {10.1093/inthealth/ihac001}, author = {Bountogo, Mamadou and Sie, Ali and Coulibaly, Boubacar and Ruder, Kevin and Chen, Cindi and Zhong, Lina and Colby, Emily and Lebas, Elodie and Deiner, Michael and Hinterwirth, Armin and Lietman, Thomas M and Seitzman, Gerami D and Doan, Thuy} } @article {1056, title = {Deep sequencing analysis of clinical samples from patients with acute infectious conjunctivitis during the COVID-19 delta surge in Madurai, India.}, journal = {J Clin Virol}, volume = {157}, year = {2022}, month = {2022 Oct 05}, pages = {105318}, abstract = {

BACKGROUND: Seasonal outbreaks of infectious conjunctivitis remain a public health issue. Determination of outbreak etiologies in the context of a worldwide pandemic may provide useful information to guide public health strategies. The aim of this study was to identify pathogens associated with outpatient infectious conjunctivitis during the COVID-19 Delta surge.

METHODS: This prospective study was conducted from April 2021 to September 2021. All outpatients presenting to the Aravind Eye Center (Madurai, India) with signs and symptoms consistent with acute infectious conjunctivitis were eligible. Three swabs were obtained from each participant: one from each conjunctiva and one from the anterior nares. Samples were processed for metagenomic RNA deep sequencing (RNA-seq).

RESULTS: Samples from 106 study participants were sequenced. The most common presenting symptoms were tearing (86\%) and itching (71\%). Preauricular lymphadenopathy was present in 38\% of participants. 20\% of participants had close contacts with similar symptoms. Systemic symptoms such as coughing, runny nose, vomiting or diarrhea were uncommonly reported. 60\% of all participants used some medicated eye drops upon enrollment. 75\% of study participants demonstrated infection with human adenovirus D (HAdV-D). 11\% of conjunctivitis was associated with SARS-CoV-2. 15\% had no definitive pathogen detected. 8\% of all participants had codetection of more than one pathogen on RNA-seq.

CONCLUSIONS: During the COVID-19 Delta surge in India, HAdV-D was the most common pathogen associated with infectious conjunctivitis. SARS-CoV-2 was the second most common associated pathogen. Seasonal surveillance may be necessary for the determination of emerging and reemerging pathogens responsible for infectious conjunctivitis.

}, issn = {1873-5967}, doi = {10.1016/j.jcv.2022.105318}, author = {Lalitha, Prajna and Prajna, N Venkatesh and Gunasekaran, Rameshkumar and Teja, Gonugunta Vishnu and Sharma, Sankalp S and Hinterwirth, Armin and Ruder, Kevin and Zhong, Lina and Chen, Cindi and Deiner, Michael and Huang, ChunHong and Pinsky, Benjamin A and Lietman, Thomas M and Doan, Thuy and Seitzman, Gerami D} } @article {901, title = {Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis.}, journal = {Cornea}, volume = {41}, year = {2022}, month = {2022 Jan 01}, pages = {39-44}, abstract = {

PURPOSE: The purpose of this article was to evaluate the impact of sample collection order on the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis.

METHODS: We performed a cross-sectional diagnostic test evaluation among subjects with infectious keratitis at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain potassium hydroxide smear, Gram stain, bacterial culture, and fungal culture, in this order. The order of MDS specimen collection relative to smear and culture samples was randomized and served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples that were diagnostic, and the agreement of MDS results with cultures.

RESULTS: MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76\%) and had 74\% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P = 0.62) or the likelihood of MDS positivity (P = 0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS corneal swabs were collected after other diagnostic corneal scrapings (P = 0.05).

CONCLUSIONS: The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared with cultures or higher susceptibility to contaminants.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Bacteria, Cornea, Cross-Sectional Studies, DNA, Bacterial, DNA, Fungal, Eye Infections, Bacterial, Eye Infections, Fungal, Female, Fungi, High-Throughput Nucleotide Sequencing, Humans, Keratitis, Male, Metagenome, Middle Aged, Specimen Handling, Young Adult}, issn = {1536-4798}, doi = {10.1097/ICO.0000000000002766}, author = {Redd, Travis K and Lalitha, Prajna and Prajna, N Venkatesh and Sikha, Misra and Gunasekaran, Rameshkumar and Hinterwirth, Armin and Chen, Cindi and Zhong, Lina and Liu, Zijun and Lietman, Thomas M and Keenan, Jeremy D and Doan, Thuy and Seitzman, Gerami D} } @article {1161, title = {Ocular Rosacea microBiome Study (ORBS)-sub-microbial versus antibiotic dosing of doxycycline versus placebo in treatment of symptomatic ocular rosacea: study protocol for a parallel-arm randomized clinical trial.}, journal = {Trials}, volume = {23}, year = {2022}, month = {2022 Dec 20}, pages = {1033}, abstract = {

BACKGROUND: Ocular rosacea is common and is often managed with long-term antibiotic treatment. Doxycycline is the most commonly selected antibiotic for the treatment of rosacea. As there is no established standard of care treatment dose for rosacea, prescribed doses of doxycycline vary widely. The FDA classifies 40\ mg daily dose of doxycycline for ocular rosacea as sub-microbial in comparison to an antibiotic dose of 200\ mg daily. However, this "sub-microbial" dose has never been evaluated in patients with ocular rosacea, and even the sub-microbial dose has potential to alter systemic mucosa flora. Here, we present a randomized controlled trial using RNA sequencing to fully characterize the impact of sub-microbial antibiotic dosing of doxycycline on antimicrobial resistance and bacterial composition of the ocular and gut flora.

METHODS: In a triple-masked parallel randomized control trial, patients with ocular rosacea will be randomized to three arms: a 40-mg dose of doxycycline, a 200-mg antibiotic dose of doxycycline, or placebo. Collected rectal and lower eyelid samples will be compared for frequency of antimicrobial resistance genetic determinants and microbiome diversity. A subjective ocular surface disease index survey and objective tear breakup time measurement will be determined.

DISCUSSION: These results will enhance our understanding of the overall systemic impact of long-term systemic sub-microbial antibiotic dosing for the treatment of chronic recurrent ocular inflammatory diseases.

TRIAL REGISTRATION: This trial was registered on ClinicalTrials.org (NCT05296837) on March 22, 2022.

}, keywords = {Anti-Bacterial Agents, Anti-Infective Agents, Doxycycline, Gastrointestinal Microbiome, Humans, Randomized Controlled Trials as Topic, Rosacea}, issn = {1745-6215}, doi = {10.1186/s13063-022-06948-9}, author = {Mahmud, Hamidah and Keenan, Jeremy D and Gonzales, John and Schallhorn, Julie and Chan, Matilda and Arnold, Benjamin and Cavallino, Victoria and Lietman, Thomas M and Doan, Thuy and Seitzman, Gerami D} } @article {1046, title = {Outpatient human coronavirus associated conjunctivitis in India.}, journal = {J Clin Virol}, volume = {157}, year = {2022}, month = {2022 Sep 27}, pages = {105300}, abstract = {

BACKGROUND: Viral conjunctivitis (pink eye) can be highly contagious and is of public health importance. There remains significant debate whether SARS-CoV-2 can present as a primary conjunctivitis. The aim of this study was to identify pathogens associated with outpatient infectious conjunctivitis during the COVID-19 Delta surge.

METHODS: This prospective study was conducted in the spring and summer months of 2021. 106 patients with acute conjunctivitis who presented to the Aravind Eye Center in Madurai, India were included. One anterior nasal swab and one conjunctival swab of each eye were obtained for each enrolled patient. Samples were subsequently processed for unbiased metagenomic RNA deep sequencing (RNA-seq). Outcomes included clinical findings and codetection of other pathogens with SARS-CoV-2 in patients with conjunctivitis.

RESULTS: Among the 13 patients identified with human coronavirus RNA fragments in their swabs, 6 patients had SARS-CoV-2 infection, 5 patients had coinfections of SARS-CoV-2 and human adenovirus (HAdV), 1 patient had a coinfection with human coronavirus OC43 and HAdV, and 1 patient had a coinfection of Vittaforma corneae and SARS-CoV-2. 30\% had bilateral disease and symptoms on presentation. Petechial hemorrhage was noted in 33\% of patients with SARS-CoV-2 infection. No patients with SARS-CoV-2 or SARS-CoV-2 and HAdV infections had subepithelial infiltrates on presentation. All patients denied systemic symptoms.

CONCLUSIONS: Among the patients presented with conjunctivitis associated with human coronavirus infection, over 50\% of the patients had co-infections with other circulating pathogens, suggesting the public-health importance of broad pathogen testing and surveillance in the outpatient conjunctivitis population.

}, issn = {1873-5967}, doi = {10.1016/j.jcv.2022.105300}, author = {Prajna, N Venkatesh and Lalitha, Prajna and Teja, Gonugunta Vishnu and Gunasekaran, Rameshkumar and Sharma, Sankalp S and Hinterwirth, Armin and Ruder, Kevin and Zhong, Lina and Chen, Cindi and Deiner, Michael and Huang, ChunHong and Pinsky, Benjamin A and Lietman, Thomas M and Seitzman, Gerami D and Doan, Thuy} } @article {916, title = {Very late onset LASIK flap Acremonium fungal keratitis confirmed by metagenomic deep sequencing.}, journal = {Am J Ophthalmol Case Rep}, volume = {25}, year = {2022}, month = {2022 Mar}, pages = {101294}, abstract = {

Purpose: To describe a unique case of LASIK flap fungal keratitis confirmed by next generation sequencing.

Observations: A 56-year-old female presented with refractory keratitis involving her LASIK flap 21 years after surgery. Confocal was positive for filamentous structures. The patient underwent immediate flap amputation followed by topical antifungal treatment. Corneal culture was positive for sp. Metagenomic deep sequencing confirmed as the primary source of infection and also identified as a likely contributor of a mixed fungal infection. Sequencing also identified hay as the likely source of the infection. Treatment resulted in eradication of the infection. The patient{\textquoteright}s final best corrected visual acuity was 20/30 with rigid contact lens overrefraction.

Conclusions: Metagenomic deep sequencing is a novel diagnostic tool that is increasingly being utilized for diagnosis of refractory keratitis. This case demonstrates the diagnostic potential of deep sequencing for identifying post-LASIK keratitis and reinforces the utility of LASIK flap amputation in the setting of tectonic flap instability due to keratolysis.

Importance: This case highlights several important clinical points for treating LASIK flap keratitis and highlights the emerging role metagenomic sequencing has in the diagnosis of infectious keratitis. This is first known case using next generation sequencing to diagnose a post-LASIK infectious keratitis.

}, issn = {2451-9936}, doi = {10.1016/j.ajoc.2022.101294}, author = {Greenwald, Miles F and Redd, Travis K and Doan, Thuy and McLeod, Stephen D and Seitzman, Gerami D} } @article {861, title = {Acute Keratoconjunctivitis Resulting From Coinfection With Avian Newcastle Virus and Human Adenovirus.}, journal = {Cornea}, year = {2021}, month = {2021 Sep 04}, abstract = {

PURPOSE: The aim of this study was to report a case of human keratoconjunctivitis caused by both Newcastle disease virus (NDV) and human adenovirus.

METHODS: A 32-year-old-man presented with an acute unilateral keratoconjunctivitis that resolved with corneal scarring. On presentation, his conjunctival swab was collected for metagenomic sequencing.

RESULTS: The highest number of pathogen sequencing reads in the conjunctival sample mapped to the NDV. The second highest number of reads mapped to human adenovirus. Confirmation testing with directed reverse-transcription polymerase chain reaction also identified NDV in the specimen.

CONCLUSIONS: Newcastle conjunctivitis has not been reported for more than 40 years. Mixed infections, including zoonotic pathogens, may be more common than realized.

}, issn = {1536-4798}, doi = {10.1097/ICO.0000000000002853}, author = {Prajna, N Venkatesh and Lalitha, Prajna and Chen, Cindi and Zhong, Lina and Lietman, Thomas M and Doan, Thuy and Seitzman, Gerami D} } @article {871, title = {Changes to ophthalmic clinical care during the coronavirus disease 2019 pandemic.}, journal = {Curr Opin Ophthalmol}, year = {2021}, month = {2021 Aug 26}, abstract = {

PURPOSE OF REVIEW: Given the impact that society as a whole, and medicine specifically, has experienced as a result of the COVID-19 pandemic, an examination of clinical care changes enacted in the field of ophthalmology is of interest to the specialty.

RECENT FINDINGS: In order to adapt to the reality of the COVID-19 pandemic, measures, such as broadening telehealth capabilities, adopting universal masking, careful sanitation procedures, applying virtual teaching in academic environments, and deferring elective surgeries were put in place. These were aimed at reducing person-to-person spread of SARS-CoV-2. Though best efforts were made at triaging ophthalmic emergencies during these times, unfortunate delays in care were observed in some circumstances. Finally, a prospective study interrogating the risk of spread at slit lamp distances for short periods of time was encouraging, suggesting low risk of transmissibility, though limited by a small case-positive sample size.

SUMMARY: Significant changes have been made in the design and delivery of ophthalmic care during the COVID-19 pandemic. Some of these, such as telemedicine, may provide value in a postpandemic world.

}, issn = {1531-7021}, doi = {10.1097/ICU.0000000000000797}, author = {Sundararajan, Miel and Schallhorn, Julie M and Doan, Thuy and Seitzman, Gerami D} } @article {906, title = {Keeping an eye on pink eye: a global conjunctivitis outbreak expert survey.}, journal = {Int Health}, year = {2021}, month = {2021 Aug 19}, abstract = {

BACKGROUND: Recurrent conjunctivitis epidemics are prevalent worldwide. Aetiologies are often undetermined.

METHODS: We surveyed conjunctivitis researchers about perceived trends in prevalence, incidence and aetiologies of conjunctivitis epidemics.

RESULTS: Of the 155 participants, 7\% endorsed globally variable and dynamic microbial aetiologies of conjunctivitis epidemics. Increased incidence of conjunctivitis epidemics over the last decade were reported by 21\% of respondents. Peak seasons differed between the northern and southern hemispheres.

CONCLUSIONS: There is regional equipoise regarding the increasing incidence and emerging underlying aetiologies of epidemic conjunctivitis. Further investigation of global surveillance and microbial characterization of conjunctivitis outbreaks could improve prevention and outcomes.

}, issn = {1876-3405}, doi = {10.1093/inthealth/ihab049}, author = {Kaur, Gurbani and Seitzman, Gerami D and Lietman, Thomas M and McLeod, Stephen D and Porco, Travis C and Doan, Thuy and Deiner, Michael S} } @article {176, title = {Evaluation of Metagenomic Deep Sequencing as a Diagnostic Test for Infectious Keratitis.}, journal = {Ophthalmology}, year = {2020}, month = {2020 Jul 17}, issn = {1549-4713}, doi = {10.1016/j.ophtha.2020.07.030}, author = {Lalitha, Prajna and Prajna, N Venkatesh and Sikha, Misra and Gunasekaran, Rameshkumar and Hinterwirth, Armin and Worden, Lee and Chen, Cindi and Zhong, Lina and Liu, Zijun and Lietman, Thomas M and Seitzman, Gerami D and Doan, Thuy} } @article {66, title = {No Time for Tears.}, journal = {Ophthalmology}, volume = {127}, year = {2020}, month = {2020 07}, pages = {980-981}, keywords = {Betacoronavirus, Coronavirus, Coronavirus Infections, COVID-19, Humans, Pandemics, Pneumonia, Viral, SARS-CoV-2, Tears, Virus Shedding}, issn = {1549-4713}, doi = {10.1016/j.ophtha.2020.03.030}, author = {Seitzman, Gerami D and Doan, Thuy} } @article {191, title = {Capnocytophaga Keratitis: Clinical Presentation and Use of Metagenomic Deep Sequencing for Diagnosis.}, journal = {Cornea}, volume = {38}, year = {2019}, month = {2019 Feb}, pages = {246-248}, abstract = {

PURPOSE: To report our experience with 2 cases of Capnocytophaga keratitis.

METHODS: This is a retrospective study of case reports. We present the clinical presentation, diagnosis, and treatment strategies of 2 patients who presented with Capnocytophaga keratitis.

RESULTS: Both patients had risk factors including systemic immune compromise and ocular trauma. Both patients had robust inflammatory keratitis with necrosis. Case 1 demonstrates identification of Capnocytophaga with traditional microbiologic techniques. Case 2 demonstrates the use of unbiased metagenomic deep sequencing for identification of this unusual corneal pathogen.

CONCLUSIONS: Capnocytophaga is a rare and aggressive infection. Even when traditional culture identifies the pathogen rapidly, keratitis can progress to perforation. In cases of severe keratitis in which traditional culture methods are unrevealing, metagenomic deep sequencing has potential to provide actionable diagnoses.

}, keywords = {Capnocytophaga, Eye Infections, Bacterial, Female, Gram-Negative Bacterial Infections, High-Throughput Nucleotide Sequencing, Humans, Keratitis, Male, Metagenome, Microbiological Techniques, Middle Aged, Retrospective Studies}, issn = {1536-4798}, doi = {10.1097/ICO.0000000000001790}, author = {Seitzman, Gerami D and Thulasi, Praneetha and Hinterwirth, Armin and Chen, Cindi and Shantha, Jessica and Doan, Thuy} } @article {76, title = {A double masked randomised 4-week, placebo-controlled study in the USA, Thailand and Taiwan to compare the efficacy of oral valganciclovir and topical 2\% ganciclovir in the treatment of cytomegalovirus anterior uveitis: study protocol.}, journal = {BMJ Open}, volume = {9}, year = {2019}, month = {2019 12 19}, pages = {e033175}, abstract = {

INTRODUCTION: Cytomegalovirus (CMV) anterior uveitis is a recognised cause of anterior uveitis in immunocompetent patients and is preventable cause of vision loss. Ocular sequelae include corneal endothelial damage which can cause corneal oedema and failure, as well as glaucoma. Recurrences of inflammation are common and therefore patients are often exposed to long-term therapy. Oral therapy is available in the form of valganciclovir, although with the caveat of systemic side effects such as bone marrow suppression and renal failure necessitating regular interval laboratory monitoring. Recent reports have demonstrated that topical 2\% ganciclovir solution may offer promising treatment outcomes in patients with CMV anterior uveitis with superior safety, cost-effectiveness and convenience profiles. An investigation into the relative equipoise of these therapies is warranted for these reasons.

METHODS AND ANALYSIS: The Systemic and Topical Control of Cytomegalovirus Anterior uveitis: Treatment Outcomes (STACCATO) trial is designed as a multicentre, block randomised by site, double-masked, placebo-controlled trial comparing the efficacy of oral valganciclovir, 2\% topical ganciclovir and placebo in treating PCR-proven CMV anterior uveitis. Participant clinical evaluation will occur at three study time points by a masked study ophthalmologist over a 28-day period to assess resolution of ocular inflammation (secondary outcome). A control group will provide additional information about the possible impact that the infected host{\textquoteright}s immune response may play in controlling local viral replication. The primary analysis is an analysis of covariance (three arms) correcting for baseline to compare quantitative CMV viral load in the anterior chamber (AC) aqueous fluid before and 7 days after treatment.

ETHICS AND DISSEMINATION: The University of California San Francisco Committee on Human Research and the Khon Kaen University Institutional Review Board have given ethical approval. The results of this trial will be presented at local and international meetings and submitted for peer-reviewed journals for publication.

TRIAL REGISTRATION NUMBER: NCT03576898.

}, keywords = {Administration, Oral, Administration, Topical, Antiviral Agents, Cytomegalovirus Infections, Double-Blind Method, Ganciclovir, Humans, Multicenter Studies as Topic, Randomized Controlled Trials as Topic, Taiwan, Thailand, United States, Uveitis, Anterior, Valganciclovir, Viral Load}, issn = {2044-6055}, doi = {10.1136/bmjopen-2019-033175}, author = {Takhar, Jaskirat S and Joye, Ashlin S and Somkijrungroj, Thanapong and Laovirojjanakul, Wipada and Lin, Chang-Ping and Lietman, Thomas M and Porco, Travis C and Keenan, Jeremy D and Gebreegziabher, Elisabeth A and Seitzman, Gerami D and Rose-Nussbaumer, Jennifer and Thuy A Doan and Acharya, Nisha R and Gonzales, John A} } @article {61, title = {Infectious corneal ulceration: a proposal for neglected tropical disease status.}, journal = {Bull World Health Organ}, volume = {97}, year = {2019}, month = {2019 Dec 01}, pages = {854-856}, keywords = {Anti-Bacterial Agents, Bacterial Infections, Corneal Ulcer, Developing Countries, Global Health, Health Promotion, Humans, Leprosy, Neglected Diseases, Onchocerciasis, Ocular, Trachoma}, issn = {1564-0604}, doi = {10.2471/BLT.19.232660}, author = {Ung, Lawson and Acharya, Nisha R and Agarwal, Tushar and Alfonso, Eduardo C and Bagga, Bhupesh and Bispo, Paulo Jm and Burton, Matthew J and Dart, John Kg and Doan, Thuy and Fleiszig, Suzanne Mj and Garg, Prashant and Gilmore, Michael S and Gritz, David C and Hazlett, Linda D and Iovieno, Alfonso and Jhanji, Vishal and Kempen, John H and Lee, Cecilia S and Lietman, Thomas M and Margolis, Todd P and McLeod, Stephen D and Mehta, Jod S and Miller, Darlene and Pearlman, Eric and Prajna, Lalitha and Prajna, N Venkatesh and Seitzman, Gerami D and Shanbhag, Swapna S and Sharma, Namrata and Sharma, Savitri and Srinivasan, Muthiah and Stapleton, Fiona and Tan, Donald Th and Tandon, Radhika and Taylor, Hugh R and Tu, Elmer Y and Tuli, Sonal S and Vajpayee, Rasik B and Van Gelder, Russell N and Watson, Stephanie L and Zegans, Michael E and Chodosh, James} } @article {186, title = {Metagenomic Deep Sequencing for the Diagnosis of Corneal and External Disease Infections.}, journal = {Ophthalmology}, volume = {126}, year = {2019}, month = {2019 12}, pages = {1724-1726}, keywords = {Adult, Aged, Aged, 80 and over, Animals, Bacteria, Conjunctival Diseases, Corneal Diseases, Eye Infections, Female, Fungi, High-Throughput Nucleotide Sequencing, Humans, Male, Metagenome, Middle Aged, Parasites, Polymerase Chain Reaction, Retrospective Studies, Scleral Diseases}, issn = {1549-4713}, doi = {10.1016/j.ophtha.2019.06.013}, author = {Seitzman, Gerami D and Hinterwirth, Armin and Zhong, Lina and Cummings, Susie and Chen, Cindi and Driver, Todd H and Lee, Michele D and Doan, Thuy} } @article {126, title = {Unbiased Pathogen Detection and Host Gene Profiling for Conjunctivitis.}, journal = {Ophthalmology}, volume = {126}, year = {2019}, month = {2019 08}, pages = {1090-1094}, abstract = {

PURPOSE: The etiology of conjunctivitis is often misdiagnosed. An ideal diagnostic test would identify all possible infectious causes. In this study, we apply unbiased metagenomic RNA deep sequencing (MDS) to identify pathogens causing conjunctivitis.

DESIGN: Molecular study of prospectively collected conjunctival swabs from patients with presumed infectious conjunctivitis.

PARTICIPANTS: Patients with presumed acute infectious conjunctivitis.

METHODS: Conjunctival swabs were collected from patients presenting with acute conjunctivitis. Swabs were processed for MDS. Pathogens were identified using a rapid computational pipeline to analyze the nonhost sequences obtained from MDS. Differential gene expression analysis was performed to evaluate for host transcriptome signatures for infectious types. Clinical samples were deidentified, and laboratory personnel handling the samples and interpreting the data were masked.

MAIN OUTCOME MEASURES: Pathogens and differential transcripts identified by MDS.

RESULTS: Metagenomic RNA deep sequencing detected pathogens in 86\% (12/14) of the patients tested. Swabs from 10 of 14 patients were positive for human adenovirus (HAdV) while swabs from 2 of 14 patients were positive for Vittaforma corneae (a parasitic fungal species of the microsporidia group). Samples positive for HAdV by RNA-seq were independently verified in a CLIA-certified laboratory. Pathogen-directed polymerase chain reaction confirmed the presence of V.\ corneae genome in the samples positive by RNA-seq. Local host transcriptome analysis identified 12 differentially expressed genes that provided distinct expression signatures for patients infected with HAdV compared with V.\ corneae.

CONCLUSIONS: Metagenomic RNA deep sequencing can reliably detect and quantify common and rare pathogens causing conjunctivitis, and identify strains. The unbiased nature of metagenomic RNA deep sequencing allowed an expanded scope of pathogen detection, including fungal species not commonly associated with acute conjunctivitis. In addition, the identification of infection type-specific local host transcriptome signatures may allow for pathogen detection even when the pathogen load is too low for direct identification.

}, keywords = {Adult, Aged, Conjunctivitis, DNA, Bacterial, DNA, Fungal, DNA, Viral, Female, High-Throughput Nucleotide Sequencing, Humans, Male, Metagenomics, Middle Aged, Young Adult}, issn = {1549-4713}, doi = {10.1016/j.ophtha.2019.03.039}, author = {Lalitha, Prajna and Seitzman, Gerami D and Kotecha, Ritesh and Hinterwirth, Armin and Chen, Cindi and Zhong, Lina and Cummings, Susie and Lebas, Elodie and Sahoo, Malaya K and Pinsky, Benjamin A and Lietman, Thomas M and Doan, Thuy} }