A rare case report of Colletotrichum gloeosporioides keratitis diagnosed by metagenomic next-generation sequencing: clinical features and diagnostic insights

Introduction

The global incidence of fungal keratitis is estimated at approximately 26.3 per 100,000 population, with higher prevalence rates reported in tropical and subtropical regions (1). This condition is characterized by significant diagnostic challenges and high invasiveness, frequently resulting in poor clinical outcomes. Studies indicate that 8–11% of affected patients ultimately require enucleation (1). To date, more than 100 microorganisms have been identified as causative agents of fungal keratitis. Among these, Fusarium, Alternaria, Aspergillus, and Candida are the most commonly reported pathogens, with extensive research available on their clinical characteristics and management (1-3). However, rare pathogens, such as Colletotrichum, are also capable of causing fungal keratitis. Due to limited reports and studies on keratitis caused by Colletotrichum gloeosporioides, clinicians often lack sufficient understanding of its unique characteristics. This knowledge gap increases the risk of misdiagnosis or delayed diagnosis, potentially compromising timely and effective treatment. Hence, it is crucial to report cases of keratitis caused by Colletotrichum, to enhance awareness and guide clinical management.

Colletotrichum is a group of pathogenic fungi that predominantly infect plants, causing significant crop yield losses and substantial economic damage. Consequently, earlier research has largely focused on its agricultural impact. However, in recent years, there has been an increasing number of reports that have highlighted Colletotrichum infections in humans. The primary sites of infection include the cornea, joints, skin, and subcutaneous tissues (4,5). The main pathogenic species implicated in human infections include C. dematium, C. coccodes, C. gloeosporioides, C. graminicola, C. crassipes, and C. truncatem (6). This study presents a case of keratitis caused by C. gloeosporioides, detailing the clinical characteristics, diagnostic process, and treatment course. The findings contribute to a deeper understanding of the clinical presentation of keratitis caused by C. gloeosporioides. We present this article in accordance with the CARE reporting checklist (https://aes.amegroups.com/article/view/10.21037/aes-25-52/rc).

Case presentation

On December 17, 2023, a 43-year-old male farmer from Guangxi presented to the Ophthalmology Department of Rongshui Miao Autonomous County People’s Hospital with complaints of vision loss in his left eye. The patient reported that 5 days earlier, his left eye had been injured by a tea-oil tree branch while working. Following the injury, he experienced an abrupt onset of blurred vision and a marked reduction in visual acuity. This was accompanied by ocular pain, excessive tearing, and lacrimation. The patient had no significant medical history and had no history of fungal infections, corneal diseases, or evidence of immunodeficiency.

Upon initial examination, the best-corrected visual acuity (BCVA) in the left eye was limited to light perception, while the BCVA in the right eye was 16/20. Slit-lamp examination of the right eye showed no abnormalities. However, the left eyelid was swollen and red, with spasmodic closure. Mixed hyperemia of the conjunctiva was observed, and fluorescein staining of the left eye was positive, with no images available. The aqueous humor appears turbid, the iris texture was blurred, the lens showed slight clouding, and the light reflex was sluggish. Notably, an 8 mm × 7 mm corneal ulcer was identified in the central cornea, extending into the stromal layer with indistinct margins (Figure 1A). B-scan ultrasonography of the fundus showed unclear visualization of the retina in the left eye.

Figure 1 Timeline of the diagnosis and treatment course. (A1-A3) Slit lamp photographs of the left eye showing an 8 mm × 7 mm central corneal ulcer extending into the stromal layer. The ulcer is characterized by lichen-white infiltration, a ground-glass appearance at the periphery, and an irregular, indistinct border. The arrows indicate corneal ulcer. (B) Colony morphology observed during fungal culture. (B1) On the third day of culture, colonies appeared villous to woolly with central black sclerotia. (B2) At the later stages of culture, the colonies transitioned to a yellow-brown to brown-gray color with a dark brown reverse side. (C) Microscopic examination of fungal structures after lactophenol cotton blue staining. (C1) Cylindrical conidia are observed alongside hyphae. (C2) A closer view highlighting the characteristic cylindrical conidia. C. gloeosporioides, Colletotrichum gloeosporioides; mNGS, metagenomic next-generation sequencing.

The conjunctival sac of the left eye was irrigated with sterile saline, and ocular secretions were collected for mycological analysis. The samples were inoculated onto Sabouraud dextrose agar and incubated at 28 and 37 ℃. Based on the clinical presentation and initial findings, the patient was treated with intravenous fluconazole and oral itraconazole. Additionally, 0.1% fluconazole and levofloxacin eye drops were applied topically to the left eye. After 3 days of incubation, filamentous, woolly fungal colonies with black sclerotia at the center were observed on the Sabouraud agar medium (Figure 1; B1). In the later stages, the colonies turned yellow-brown to gray-brown, with a dark brown reverse (Figure 1; B2). Microscopic examination using lactophenol cotton blue staining revealed numerous capsule-shaped conidia and characteristic brown, variably shaped appressoria (Figure 1C). Identification of the specific fungal subtype could not be achieved based solely on colony morphology. To accurately identify the fungus, we employed the Autof MS 1000 automated microbial mass spectrometry system. Among the results, C. gloeosporioides received the highest score (5.821), yet this value was close to those of other microorganisms within the same genus as well as from different genera, making the identification unreliable. Ultimately, metagenomic next-generation sequencing (mNGS) was utilized, which confirmed the isolate as C. gloeosporioides with a high gene coverage rate of 57.91% (Figure 2). Based on these findings, the patient was ultimately diagnosed with fungal keratitis caused by C. gloeosporioides. The patient’s treatments were adjusted to include 5% natamycin antifungal therapy (every 2 hours during the day and every 4 hours at night), pranoprofen eye drops for anti-inflammation (every 6 hours), and 0.5% levofloxacin eye drops for infection control (every 4 hours). By the eighth day of treatment, the corneal ulcer had reduced to 6 mm × 5 mm, and the patient showed overall clinical improvement. No adverse reactions occurred throughout the entire course of diagnosis and treatment. On December 25, 2023, after a 9-day hospital stay, the patient was discharged with a prescription for continued medications, following consultation with a specialist physician. To assess the recovery, we conducted a telephone follow-up in December 2025. The patient reported significant improvement in visual acuity in the left eye compared to the time of admission, with complete resolution of previous symptoms such as eye pain, photophobia, tearing, and foreign body sensation. Based on the full remission of these symptoms, it is clinically inferred that the corneal ulcer is entering the healing phase or has healed. At the time of follow-up, the patient indicated no signs of recurrence.

Figure 2 The mNGS result of the fungal colonies. Coverage graph of Colletotrichum gloeosporioides. The abscissa represents the genome position, the left ordinate is the number of reads of the pathogen aligned on the genome location (number of map reads shown in blue), and the right ordinate is the average sequencing depth at the corresponding position (depth, the red line in the figure). mNGS, metagenomic next-generation sequencing.

Ethical considerations

All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee(s) and with the Declaration of Helsinki and its subsequent amendments. Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal. Medical Ethics Committee of Rongshui Miao Autonomous County People’s Hospital has passed the ethics approval (No. 2024218).

Discussion

The present study presents a case of fungal keratitis caused by C. gloeosporioides infection. The genus Colletotrichum, commonly referred to as anthracnose fungus, is taxonomically classified within the fungal hierarchy under Ascomycota, Pezizomycotina, Sordariomycetes, Hypocreomycetidae, Glomerellales, and Glomerellaceae. To date, the genus has been identified to include 248 species and 14 species complexes (7). As one of the most prevalent plant pathogens, anthracnose fungi cause a wide range of diseases in herbaceous and woody plants. Particularly vulnerable are food crops, fruits, vegetables, and ornamental plants, leading to reduced yields and substantial economic losses. Due to its widespread distribution, destructive potential, and scientific significance, Colletotrichum ranks as the eighth most important fungal group in terms of economic and scientific relevance, according to plant pathologists (8).

In addition to its role as a plant pathogen, Colletotrichum has been associated with human infections. Species reported to cause human keratitis include C. gloeosporioides, C. truncatum, C. coccodes, C. dematium, C. graminicola, and C. crassipes. Among these, C. gloeosporioides stands out as a significant species complex capable of infecting over 1,000 crop varieties. It affects plant branches, leaves, and fruits, often causing severe outcomes such as fruit decay, plant wilting, and even death (9,10). The first human keratitis case caused by C. gloeosporioides was reported by Japanese researchers in 2001. Since then, additional cases have been documented in India, Spain, China, and other regions (6,11-19). A review of previously reported cases reveals that most corneal ulcers caused by keratitis due to Colletotrichum fungal infection were confined to the stromal layer. However, some cases involved ulcers breaching the stromal layer, extending to the Descemet membrane and endothelial layer. Such cases typically exhibit more rapid progression of vision loss and poorer prognoses (Table S1). In our case, the corneal ulcer was limited to the stromal layer, yet the patient experienced severe vision impairment, retaining only light perception despite treatment. This discrepancy may be attributed to the large ulcer size (8 mm × 7 mm). However, additional clinical data are needed to explore this hypothesis further and better understand the factors influencing outcomes in keratitis caused by Colletotrichum fungal infection.

We observed that the severity of keratitis caused by C. gloeosporioides varies significantly depending on the source of the injury. Cases caused by plant injuries often result in more severe vision impairment, with some patients ultimately requiring enucleation (13). Among the currently reported cases (Table S1), plant-related trauma represents the most common predisposing factor for C. gloeosporioides keratitis, accounting for 56.25% of cases. Notably, compared with infections arising from non-plant-related causes, plant-associated injuries show a substantially higher proportion of severe visual impairment—including eye evisceration, light perception only, or the need for penetrating keratoplasty (80% vs. 25%), suggesting a markedly worse clinical prognosis. Studies indicate that many plant branches and leaves infected with C. gloeosporioides harbor high concentrations of the fungus (20,21). Direct contact with these contaminated plant materials can scratch the cornea and inoculate fungal spores, leading to rapid disease progression and a poor prognosis. In agricultural regions, individuals are more likely to come into contact with infected plants. These areas often have limited access to advanced medical care, contributing to clinical heterogeneity in keratitis caused by C. gloeosporioides. Diagnosing fungal keratitis based solely on clinical presentation can be challenging.

Several studies have demonstrated that plant-related ocular trauma is a major predisposing factor for fungal keratitis, particularly in tropical and subtropical regions (22). In climates conducive to fungal growth, such as tropical/subtropical zones, fungi are more frequently isolated than bacteria in corneal ulcers following plant or vegetative trauma (23,24). This underscores the importance of accurately identifying C. gloeosporioides for timely diagnosis and treatment. In the present case, the patient reported that the fungal infection occurred following an eye injury caused by a branch. It is suspected that the branch was contaminated with C. gloeosporioides or that the patient inadvertently transferred fungal spores to the eye by rubbing it with unclean hands. By the time the patient sought medical attention, the lesion had expanded, with significant infiltration depth.

In cases of corneal infection where antibiotics fail to yield results, clinicians must consider the possibility of fungal keratitis. Previous studies emphasize that early diagnosis and treatment are crucial for managing fungal keratitis. Delayed intervention allows for extensive fungal hyphal proliferation and deeper infection, substantially increasing treatment difficulty and risking severe vision loss. This can significantly impact the patient’s quality of life and daily functioning. Given these factors, greater attention must be directed toward the diagnosis and management of keratitis caused by C. gloeosporioide fungal infections.

As primary laboratory technicians, it is crucial to enhance our skills in identifying fungal species through detailed analysis of colony characteristics and microscopic morphology. A comprehensive understanding of the submission, culturing processes of microbial specimens, and the sources of patient infections is equally important. Strengthening our capacity to accurately identify and differentiate fungi will enable us to assist clinicians more effectively in locking down the pathogens, thereby improving the efficiency of clinical diagnosis and treatment. In previous studies on C. gloeosporioide keratitis, Mitani et al. [2011] and Hung et al. [2020] primarily relied on culturing and high-resolution confocal microscopy (HRT-RCM) to observe fungal hyphae (6,12). However, these methods require high technical skill and precision. While mass spectrometry has become a valuable tool in microbial identification, it has certain limitations when distinguishing related species or subtypes, especially due to high genetic homology within species. These limitations are compounded by the relatively narrow scope of available databases, which may not cover all subtypes, thereby reducing the accuracy of identification in some cases. The mNGS technology proven to be a valuable tool in species identification due to its speed, efficiency, and convenience. This advanced technology facilitates in-depth sequencing and precise analysis of complex biological samples, accurately identifying the species present. By significantly reducing the identification timeline and enhancing accuracy, mNGS has emerged as a pivotal method in pathogen detection and clinical microbiology. Initially, we employed mass spectrometry to identify the colonies, but this approach yielded no definitive results, providing only a tentative indication of C. gloeosporioides. We subsequently used mNGS, which successfully identified the specific pathogen. These findings suggest that mNGS offers greater accuracy and advantages over mass spectrometry for this purpose. For patients requiring early clarification of the causative pathogen, mNGS can be used as an early auxiliary diagnostic tool and combined with traditional microbiological methods to provide a more comprehensive assessment. However, the cost of mNGS is relatively high, which may further increase the financial burden on patients.

This report presents a rare case of C. gloeosporioides keratitis in southern China, contributing valuable clinical evidence on human infections by this genus. The case involved a relatively large corneal ulcer, providing insights into the impact of ulcer size on disease severity and visual outcomes. We detail the diagnostic workflow, comparing fungal culture, microscopy, mass spectrometry, and mNGS, and demonstrate the superior accuracy of mNGS for identifying rare pathogens when conventional methods are inconclusive.

This study has several limitations. First, antifungal susceptibility testing was not performed on cultured isolates. However, the selection of antifungals was based on prior reports and known resistance patterns; reported C. gloeosporioides and other filamentous fungal isolates generally exhibit good in vitro susceptibility to amphotericin B, itraconazole, voriconazole, micafungin, and natamycin (12,15). Second, the identification of C. gloeosporioides was not confirmed using molecular techniques such as polymerase chain reaction (PCR) or Sanger sequencing. Finally, a limitation of this case report is the lack of more objective and systematic follow-up data. Although we conducted a follow-up phone call with the patient, the information obtained was primarily based on the patient’s subjective report, which may somewhat limit the assessment of long-term outcomes, such as visual acuity recovery and corneal status.

Conclusions

We report a rare case of keratitis caused by C. gloeosporioides in southern China. Our findings indicate that fungal keratitis resulting from plant-related trauma tends to present with more severe clinical symptoms and a poorer prognosis. Furthermore, the size of the corneal ulcer appears to play a critical role in determining the patient’s visual recovery. In terms of diagnosis, mNGS has the potential to serve as an effective tool for the rapid identification of rare ocular infections. The study highlights the challenges of diagnosing plant-related ocular infections and offers practical guidance for laboratory personnel in specimen handling and fungal identification, providing useful experience for improving clinical diagnosis and treatment strategies.

Acknowledgments

The authors would like to thank the team of Infection Diagnosis Center in Guangxi KingMed Diagnostics for their help for in metagenomic next-generation sequencing report interpretation and experimental procedure.

Footnote

Reporting Checklist: The authors have completed the CARE reporting checklist. Available at https://aes.amegroups.com/article/view/10.21037/aes-25-52/rc

Peer Review File: Available at https://aes.amegroups.com/article/view/10.21037/aes-25-52/prf

Funding: This study was funded and supported by Guangxi Health Commission Self-Funded Scientific Research Project (No. Z-B20231561) and Nanning City Science Research and Technology Development Program (No. 20233071).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://aes.amegroups.com/article/view/10.21037/aes-25-52/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee(s) and with the Declaration of Helsinki and its subsequent amendments. Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal. Medical Ethics Committee of Rongshui Miao Autonomous County People’s Hospital has passed the ethics approval (No. 2024218).

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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