Article
Shotgun metagenomic sequencing in culture negative microbial keratitis
Author/s | Borroni, Davide
Bonzano, Chiara Sánchez González, José María Rachwani-Anil, Rahul Zamorano Martín, Francisco Pereza Nieves, Jorge Traverso, Carlo Enrico García Lorente, María Rodríguez-Calvo-de-Mora, Marina Espósito, Alfonso Godin, Fernando Rocha de Lossada, Carlos |
Department | Universidad de Sevilla. Departamento de Física de la Materia Condensada Universidad de Sevilla. Departamento de Cirugía |
Publication Date | 2023-07 |
Deposit Date | 2023-12-14 |
Published in |
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Abstract | Purpose: To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. Methods: DNA of microbial keratitis samples were collected ... Purpose: To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. Methods: DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. Results: 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. Conclusions: Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples. |
Citation | Borroni, D., Bonzano, C., Sánchez González, J.M., Rachwani-Anil, R., Zamorano Martín, F., Pereza Nieves, J.,...,Rocha de Lossada, C. (2023). Shotgun metagenomic sequencing in culture negative microbial keratitis. European Journal of Ophthalmology, 33 (4), 1589-1595. https://doi.org/10.1177/11206721221149077. |
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