Table 1.
Omics approach for diagnosing fungal keratitis.
| Eyes (n) | Subjects a | Detection Target | Technique b | Pathogen Identification c | Reference | |
|---|---|---|---|---|---|---|
| Sensitivity | Specificity | |||||
| Genomics | ||||||
| 30 | CSMK | 18S rRNA gene | Nested PCR | 94% (15/16) | 50% (7/14) | Gaudio et al. [42] |
| 32 | CSFK | ITS2−5.8S rRNA gene | Nested PCR | 93% (14/15) | 24% (4/7) | Ghosh et al. [43] |
| 30 | CSMK | 18S rRNA gene | PCR | 88% (10/11) | 82% (18/19) | Embong et al. [44] |
| 66 | CSFK | 18S rRNA gene | PCR | 94% (29/31) | 17% (6/35) | Kim et al. [45] |
| 40 | CSFK | 28S rRNA gene | PCR | 70% (7/10) | 57% (17/30) | Vengayil et al. [31] |
| 28 | CSFK | 18S rRNA gene | Nested PCR | 81% (13/16) | 33% (4/12) | Badiee et al. [46] |
| 39 | CSMK | ITS2 & EF1-alpha gene, Cap5G & Cap8G gene, LytA gene, gyrB gene, mecA gene | Real-time PCR | 100% (3/3) | 94% (34/36) | Itahashi et al. [47] |
| 20 | DFK | ITS1-5.8S rRNA gene-ITS2 | Semi-nested PCR | 92.6% (25/27) | N.A. | Ferrer et al. [48] |
| 38 | CSMK | 18S rRNA gene | Real-time PCR-HRM | 100% (10/10) | 75% (21/28) | Goldschmidt et al. [49] |
| 50 | CSMK | 18S rRNA gene-ITS1-5.8S rRNA gene-ITS2-28S rRNA gene | DHA | 100% (20/20) | 97% (29/30) | Kuo et al. [50] |
| 67 | CSMK | ITS1-5.8S rRNA gene-ITS2 | Direct PCR | 96% (23/24) | 24% (9/38) | Zhao et al. [51] |
| 42 | CSFK | Mitochondrial cytochrome b gene | Multiplex PCR | 88% (37/42) | N.A. | He et al. [52] |
| 559 | CSFK | 18S rRNA gene-ITS1-5.8S rRNA gene-ITS2-28S rRNA gene | Multiplex PCR | 89% (423/473) | N.A. | Manikandan et al. [53] |
| Metagenomics | ||||||
| 1 | CSFK | Tagged DNA-DNA fragment-tagged DNA | PCR, Shot-gun sequencing | N.A. | N.A. | Shigeyasu et al. [54] |
| 18 | FK | V3-V4 region of 16S rRNA gene | PCR, 16S rDNA sequencing | N.A. | N.A. | Ge et al. [55] |
| 63 | FK | ITS2−5.8S rRNA gene, V3-V4 region of 16S rRNA gene | PCR, ITS2 & 16S rDNA sequencing | N.A. | N.A. | Kalyana Chakravarthy et al. [56] |
| Proteomics | ||||||
| 56 | FK | Tear proteins | 2D-PAGE, MALDI-TOF MS | N.A. | N.A. | Ananthi et al. [38] |
| 88 | Fusarium keratitis | Tear proteins | 2D-DIGE, LC-MS/MS | N.A. | N.A. | Ananthi et al. [39] |
| 16 | Aspergillus keratitis | Tear proteins | 1D-PAGE, in-gel digestion, LC-MS/MS | N.A. | N.A. | Kandhavelu et al. [57] |
aCSMK = clinically suspected microbial keratitis; CSFK = clinically suspected fungal keratitis; DFK = definite fungal keratitis; b PCR = polymerase chain reaction; HRM = high resolution melting analysis; DHA = dot hybridization assay; 2D-PAGE = two-dimensional polyacrylamide gel electrophoresis; MALDI-TOF MS = matrix-assisted laser desorption/ionization-time of flight mass spectrometry; 2D-DIGE = two-dimensional difference gel electrophoresis; LC-MS/MS = Liquid chromatography-tandem mass spectrometry; c Diagnostic standard based on microbial culture or DNA sequencing; N.A. = not available; rRNA = ribosomal RNA; ITS = internal transcribed spacer.