Aqueous Humor mNGS Identifies a Hidden Pathogen in Chronic Ocular GVHD
A chronic ocular graft-versus-host disease case turned on a diagnosis that standard microbiology could not make. In a 35-year-old man with prior allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia, progressive ocular surface disease evolved into a right-eye corneal ulcer, hypopyon, and mild vitreous haze — a combination that pushed the working diagnosis beyond severe keratitis and into endophthalmitis.
The decisive signal came from aqueous humor metagenomic next-generation sequencing, which detected Staphylococcus epidermidis with 5,543 unique reads and 12.3% genome coverage, without any co-pathogens. Conventional Gram stain, potassium hydroxide mount, and bacterial and fungal cultures were negative. In an immunosuppressed host with a damaged corneal barrier, that kind of diagnostic gap has immediate bedside consequences: empiric therapy can miss the true organism while ocular destruction continues.
Corneal Breakdown After Allo-HSCT Set the Stage for Intraocular Infection
The patient’s ocular history fit chronic oGVHD. He presented after 10 months of bilateral redness, photophobia, and dryness, and his exam showed eyelid-margin congestion, keratinization, meibomian gland orifice blockage, punctal occlusion, corneal edema, opacity, and epithelial defects in both eyes. Schirmer testing measured 1 mm in one eye and 2 mm in the other, confirming severe aqueous tear deficiency. Visual acuity at that stage had already fallen to light perception in the right eye and hand motion at 33 cm in the left eye, with elevated intraocular pressure in the right eye.
Initial management focused on suppressing ocular surface inflammation and restoring epithelial integrity. Topical prednisolone acetate, cyclosporine, and tacrolimus were used alongside autologous serum and sodium hyaluronate eye drops. The ocular surface improved enough for discharge, with vision measured at 20/100 in the right eye and 20/40 in the left eye after 10 days.
Three months later, the right eye deteriorated abruptly with pain and vision loss over 2 days. Central corneal ulceration measured approximately 4 × 2 mm and a 1-mm hypopyon was present. B-scan ultrasonography demonstrated mild vitreous haze. In a patient receiving systemic immunosuppression, even limited vitreous opacification changes the diagnostic frame: the infection is no longer confined to the cornea.
Diagnostic Failure by Culture, Diagnostic Clarity by Sequencing
An anterior chamber puncture was performed after antiseptic preparation with 5% povidone-iodine and strict sterile technique. Empiric therapy began with intravenous cefuroxime and frequent topical antibiotics, but the ocular inflammation worsened within 3 days, with a corneal endothelial plaque appearing despite treatment. Confocal microscopy showed no fungal organisms. Routine blood work, C-reactive protein, and erythrocyte sedimentation rate were normal, and the absence of fever or chills made endogenous sepsis unlikely.
The aqueous humor mNGS result changed the course of care. S. epidermidis was interpreted as the causative pathogen because the sequencing signal was strong, the clinical picture fit bacterial endophthalmitis, no fungal or viral organisms were found, and negative controls did not show the organism. A read count above the threshold used for bacterial pathogens in immunocompromised post-allo-HSCT patients supported clinical significance rather than contamination.
This matters because coagulase-negative staphylococci can be dismissed too easily when culture is negative. In a compromised ocular surface, however, S. epidermidis is fully capable of deep invasion, and the organism’s low-grade commensal reputation can delay intervention until the eye is structurally threatened.
Targeted Vancomycin Controlled the Infection Without Vitrectomy
Therapy shifted immediately to targeted vancomycin. The regimen included vancomycin injection into the vitreous cavity, anterior chamber, and periorbital region, along with intravenous vancomycin at 0.5 g twice daily. Topical treatment added hourly moxifloxacin eye drops, gatifloxacin eye gel three times daily, and daily periocular vancomycin injections. The intravitreal dosing approach followed established protocols for Gram-positive endophthalmitis, and vancomycin was chosen for its dependable activity against coagulase-negative staphylococci.
Systemic steroids were tapered and discontinued after discussion with hematology, and oral mycophenolate mofetil was added to cyclosporine to preserve graft-versus-host disease control while lowering steroid-driven infectious risk. That adjustment reflects the central tension in chronic oGVHD: immune suppression protects against alloimmunity, yet excessive immunosuppression can leave a heavily damaged ocular surface defenseless against invasive infection.
The response was clinically meaningful. After 10 days of targeted vancomycin therapy, the corneal ulcer gradually healed and the hypopyon resolved. Infection control was achieved without corneal perforation, without therapeutic vitrectomy, and without enucleation. For a case like this, avoiding posterior segment surgery is not a cosmetic victory; it preserves ocular architecture in a host already living with severe surface failure.
Amniotic Membrane Transplantation Addressed the Residual Surface Defect
Infection control did not end the problem. A persistent epithelial defect and corneal bullae caused severe blepharospasm and unbearable pain, so amniotic membrane transplantation was performed after the infection was contained. The procedure was used to support epithelial healing, not as antimicrobial treatment. Pain improved on the first postoperative day, and the patient could open the eye freely.
At 1.5 years of follow-up, the right cornea remained transparent with minimal neovascularization, and the patient stayed asymptomatic in daily life. Best-corrected visual acuity was 20/400 in the right eye and 20/40 in the left eye. He continued topical cyclosporine twice daily and sodium hyaluronate three times daily, with no reported adverse effects or interruptions.
The long-term outcome was anatomically favorable despite residual visual loss in the affected eye. Corneal integrity was preserved, and the disease course stopped short of perforation, vitreous surgery, or eye removal.
Why This Case Extends Beyond a Single Eye Infection
Chronic oGVHD creates a narrow biological margin for safety. Tear deficiency, epithelial breakdown, meibomian gland dysfunction, punctal occlusion, and chronic inflammation compromise the cornea before infection even begins. Once the surface barrier fails, organisms that are usually low-virulence can reach deeper ocular compartments, especially under corticosteroid exposure and systemic immune suppression.
Aqueous humor mNGS offers something conventional microbiology often cannot: pathogen identification from a small-volume intraocular sample within a clinically useful window. In this case, that speed mattered because the organism was not recovered by culture, yet treatment had to be escalated before structural loss became irreversible. The sequencing result gave a bacterial target, narrowed therapy to vancomycin, and supported withdrawal of local calcineurin-inhibitor drops during the acute infection.
The report also reinforces a broader point for transplant ophthalmology. When corneal ulceration, hypopyon, and vitreous haze occur in chronic oGVHD, clinicians should think beyond surface keratitis alone. Intraocular extension can be present even when systemic inflammatory markers are quiet and blood cultures are not helpful. For immunosuppressed patients, an apparently small diagnostic window can decide whether the eye is saved intact or moves toward surgical salvage.