The Human Ocular Surface Fungal Microbiome

Shivaji, Sisinthy; Jayasudha, Rajagopalaboopathi; Prashanthi, Gumpili Sai; Chakravarthy, Sama Kalyana; Sharma, Savitri

doi:10.1167/iovs.18-26076

Cited by 61 publications

(61 citation statements)

References 43 publications

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“…A question that has not been addressed is whether changes or dysbiosis in the ocular microbiome accompanies the diseased state of the eye. Conventional culture-based and PCR-based methods of conjunctival swabs and corneal scrapings did not yield fungi in > 80% of the samples analysed [16,17,18,19]. The common fungi in the culture positive ocular surface samples included Alternaria sp., Fusarium sp., Aspergillus niger , Aspergillus flavus , Curvularia sp., Penicillium sp., Helminthosporium sp., Candida albicans , C. guilliermondii , C. parapsilosis , Saccharomyces cerevisiae , Hormodendrum sp., and Rhodotorula rubra .…”

Section: Introductionmentioning

confidence: 99%

“…The common fungi in the culture positive ocular surface samples included Alternaria sp., Fusarium sp., Aspergillus niger , Aspergillus flavus , Curvularia sp., Penicillium sp., Helminthosporium sp., Candida albicans , C. guilliermondii , C. parapsilosis , Saccharomyces cerevisiae , Hormodendrum sp., and Rhodotorula rubra . In contrast, when the fungal microbiome of the ocular surface of healthy individuals was analysed by Next generation sequencing (NGS), using internal transcribed spacer 2 (ITS2) sequencing as a proxy for fungi, the method identified fungi in 73.5% swabs, detected 65 distinct genera with Aspergillus , Setosphaeria , Malassezia , and Haematonectria in all the studied eyes [19]. Further Alpha diversity in the two eyes was similar and sex had no effect, but Chao 1 and Simpson indices were altered by age [19].…”

Section: Introductionmentioning

confidence: 99%

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Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

et al. 2019

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Keratitis, an inflammatory disease of the eye, when neglected could lead to sight-threatening complications and ultimately blindness. Globally, over a million people are affected by keratitis annually. Keratitis has a microbial etiology and is caused by bacteria, fungi, viruses, etc. The present study compared the ocular surface fungal microbiome of healthy individuals and individuals with fungal keratitis. Fungal microbiomes from the conjunctival swabs of healthy individuals and from conjunctival swabs and corneal scrapings of individuals with fungal keratitis were generated using ITS2 region amplicons. Microbiomes were sequenced using Illumina MiSeq 2 × 250 base pair chemistry with a paired-end protocol. Based on Alpha diversity indices, phylum and genera level diversity, abundance differences, and heat map analysis, the fungal microbiomes of conjunctival swabs and corneal scrapings of individuals with fungal keratitis exhibited dysbiosis (alterations in the diversity and abundance) compared to the ocular surface microbiome of the healthy control individuals. This is the first report indicating dysbiosis in the fungal microbiome of conjunctival swabs and corneal scrapings in individuals with fungal keratitis. A total of 11 genera present in the majority of the eyes constituted the variable core ocular microbiome.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

et al. 2019

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“…In our study, the CNS was also most predominant in the cultures of CL cases. When 16S r-DNA sequencing was analyzed for conjunctival flora, Proteobacteria was reported as the most abundant phyla (64.4%) 13 . This is also consistent with our metagenomic analysis (Fig.…”

Section: Discussionmentioning

confidence: 99%

Presence of Acanthamoeba and diversified bacterial flora in poorly maintained contact lens cases

Miyazaki

Eguchi

Kuwahara

et al. 2020

Sci Rep

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Acanthamoeba can cause visually destructive Acanthamoeba keratitis (AK) in contact lens (CL) users. The purpose of this study was to determine whether Acanthamoeba was present in the CL cases of CL wearers and to develop techniques to prevent the contaminations. To accomplish this, 512 CL case samples were collected from 305 healthy CL wearers. Using real-time PCR, Acanthamoeba DNA was detected in 19.1% of CL cases, however their presence was not directly associated with poor CL case care. Instead, the presence of Acanthamoeba DNA was associated with significant levels of many different bacterial species. When the CL cases underwent metagenomic analysis, the most abundant bacterial orders were Enterobacteriales followed by Burkholderiales, Pseudomonadales, and Flavobacteriales. The presence of Acanthamoeba was characterized by Propionibacterium acnes and Rothia aeria and was also associated with an increase in the α diversity. Collectively, Acanthamoeba contamination occurs when a diversified bacterial flora is present in CL cases. This can effectively be prevented by careful and thorough CL case care. Acanthamoeba is a free-living amoeba and is a representative pathogen that can cause keratitis. Acanthamoeba keratitis (AK) is a visually devastating disease and is refractory to conventional treatments. Thus, AK often requires corneal transplantation. Acanthamoeba can also cause granulomatous amoebic encephalitis (GAE). Although the incidence of GAE is rare, the mortality rate is almost 90% because of difficulties in diagnosing and treating it 1. AK is known to have strong associations with poor care of contact lenses (CL) and CL cases. When CL users engage in water activities, e.g., bathing or swimming, while wearing CL, there is a significant risk of AK 2,3. Acanthamoeba is a ubiquitous microorganism that is found in water supply systems, water sources including rivers, lakes, swimming pools, and also in soil 4,5. It has been reported that Acanthamoeba contamination of the rivers supplying water to the population was the cause of increased AK occurrences 6. For example, the river water supply in Iran was contaminated with Acanthamoeba, and almost 22% of river samples were PCR-positive for Acanthamoeba 6. In an analysis of the drinking water storage towers of Paris, approximately 20 to 25 Acanthamoebae were detected per liter 1. Thus, tap water can pose risks for AK contact together with inappropriate CL care for the general population without engagement in water activity 7,8 .

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“…Fourth, ITS sequencing can only identify fungal pathogens of FK rather than diagnose FK. Fifth, the positive rate of ITS sequencing is not significantly improved compared with culture, partly due to the scarce quantity of collected fungi, choice of reagents and kits, and PCR bias 34 . www.nature.com/scientificreports www.nature.com/scientificreports/ Divergence between culture and ITS sequencing.…”

Section: Culture For Identification Of Causative Fungi a Successful mentioning

confidence: 99%

Diagnostic information Profiling and Evaluation of Causative Fungi of Fungal Keratitis Using High-throughput Internal Transcribed Spacer Sequencing

Ren¹,

Liu²,

Wang³

et al. 2020

Sci Rep

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Early and accurate diagnosis is essential for the targeted management of fungal keratitis (FK), which is one of the major blinding eye diseases worldwide. To elucidate the diagnostic information of high-throughput internal transcribed spacer (ITS) sequencing for identifying causative fungi of FK, 38 patients who were highly suspected of having FK were included in this research. In vivo confocal microscopy, potassium hydroxide smear, and fungal culture were performed to diagnose FK. Culture and ITS sequencing were used to identify causative fungi. We hypothesized that the dominant genus was the result of pathogen identification by ITS sequencing. Thirty-five patients were eventually diagnosed with FK, with fungal pathogens found by confocal microscopy in 27 patients (77.14%), by smear examination in 27 patients (77.14%), by culture in 25 patients (71.43%), and by ITS sequencing in 26 patients (74.29%). Eight causative fungal genera were determined by ITS sequencing, while five causative fungal genera were identified based on the morphology of the cultured pathogens. The results of ITS sequencing and culture were coincident in 10 patients with FK (28.57%). It is concluded that ITS sequencing, to some extent, challenged fungal culture and might be an optional complement in identifying fungal pathogens in corneas.

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The Human Ocular Surface Fungal Microbiome

Cited by 61 publications

References 43 publications

Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

Presence of Acanthamoeba and diversified bacterial flora in poorly maintained contact lens cases

Diagnostic information Profiling and Evaluation of Causative Fungi of Fungal Keratitis Using High-throughput Internal Transcribed Spacer Sequencing

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