Metagenomic analysis for detecting  Fusarium solani  in a case of fungal keratitis

Shigeyasu, Chika; Yamada, Masakazu; Aoki, Kotaro; Ishii, Yoshikazu; Tateda, Kazuhiro; Yaguchi, Takashi; Okajima, Yukinobu; Hori, Yuichi

doi:10.1016/j.jiac.2017.12.019

Cited by 13 publications

(14 citation statements)

References 12 publications

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“…MDS could be used in patients with difficult-to-diagnose infections, as a front-line diagnostic tool. In difficult-to-culture samples, metagenomic shotgun is a promising test for the identification of microbial keratitis and undiagnosed encephalitis 92 93. Together with uveitis-related disorders, the microbiome study can potentially and dramatically change the management and treatment of these diseases.…”

Section: Discussionmentioning

confidence: 99%

Metagenomics in ophthalmology: current findings and future prospectives

et al. 2019

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Less than 1% of all microorganisms of the available environmental microbiota can be cultured with the currently available techniques. Metagenomics is a new methodology of high-throughput DNA sequencing, able to provide taxonomic and functional profiles of microbial communities without the necessity to culture microbes in the laboratory. Metagenomics opens to a ‘hypothesis-free’ approach, giving important details for future research and treatment of ocular diseases in ophthalmology, such as ocular infection and ocular surface diseases.

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Section: Discussionmentioning

confidence: 99%

Metagenomics in ophthalmology: current findings and future prospectives

et al. 2019

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“…Pneumocystis jirovecii is the predominant fungus reported (~25% of the fungi detected), followed by Aspergillus species (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively~5%) (Figure 2). Excluding P. jirovecii, which is generally unculturable, out of the remaining 274 fungi detected by NGS, only 105 (~38%) were recovered by fungal culture from the same or different specimens from the respective patients [26,[29][30][31][32][33][34][35][36][37][38][39]43,45,46,49,52,54,57,59,62,64,66,67,71,73,76,77]. cies (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively ~5%) (Figure 2).…”

Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

“…cies (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively ~5%) (Figure 2). Excluding P. jirovecii, which is generally unculturable, out of the remaining 274 fungi detected by NGS, only 105 (~38%) were recovered by fungal culture from the same or different specimens from the respective patients [26,[29][30][31][32][33][34][35][36][37][38][39]43,45,46,49,52,54,57,59,62,64,66,67,71,73,76,77]. The majority of P. jirovecii infections diagnosed by NGS were reported in case series [34,36,39,41,48,53,55,58,62,64,65,67,72,75].…”

Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

“…Lastly, publications were searched using specific fungal names and after manual examination five extra articles were added. Therefore, in total 52 articles were included in this review [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ].…”

Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

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Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Tsang

Teng

Lau

et al. 2021

JoF

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Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.

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“…Shigeyasu et al reported a difficult-to-identify and medically refractory case of FK, confirmed by metagenomic analysis with corneal scraping and aqueous fluid samples [54]. The authors adopted metagenomic shotgun next-generation sequencing by a MiSeq platform (Illumina, Inc., CA, USA) and a cloud-computing pipeline MePIC for pathogen identification.…”

Section: Diagnosing or Investigating Fk By An Omics Approachmentioning

confidence: 99%

An Omics Approach to Diagnosing or Investigating Fungal Keratitis

Kuo

Chen

Hsu

et al. 2019

IJMS

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Fungal keratitis (FK) is one of the most severe corneal infectious diseases. FK often leads to poor visual prognosis and thus requires accurate diagnosis. Conventional approaches, including clinical diagnoses, smears, and cultures, often fail to provide reliable diagnostic value. Omics approaches, such as those using genomic, metagenomic, and tear proteomic data sources, provide promising features for improving the diagnosis and monitoring the progression of FK. Genomic approaches are based mainly on detecting amplicons of ribosomal RNA genes, and internal transcribed spacers are gradually gaining popularity in clinical practices. A metagenomic approach based on 16S rRNA genes may help monitor the dynamic change of conjunctival microbiota associated with an FK event, whereas that based on shot-gun and 18S rRNA target enrichment sequencing could have the potential to diagnose FK using clinical samples. A tear proteomic approach may provide comprehensive information about ocular surface defense and injury during FK. Representative up- and down-regulated proteins during FK could also be used as biomarkers to determine the clinical course and develop a treatment strategy in different stages of FK. Consequently, a personalized tear proteomic approach will soon play a key role in FK management.

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Metagenomic analysis for detecting Fusarium solani in a case of fungal keratitis

Cited by 13 publications

References 12 publications

Metagenomics in ophthalmology: current findings and future prospectives

Metagenomics in ophthalmology: current findings and future prospectives

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

An Omics Approach to Diagnosing or Investigating Fungal Keratitis

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