TY - JOUR
T1 - Shotgun metagenomic sequencing in culture negative microbial keratitis
AU - Borroni, Davide
AU - Bonzano, Chiara
AU - Sánchez-González, José María
AU - Rachwani-Anil, Rahul
AU - Zamorano-Martín, Francisco
AU - Pereza-Nieves, Jorge
AU - Traverso, Carlo Enrico
AU - García Lorente, María
AU - Rodríguez-Calvo-de-Mora, Marina
AU - Esposito, Alfonso
AU - Godin, Fernando
AU - Rocha-de-Lossada, Carlos
N1 - Publisher Copyright:
© The Author(s) 2023.
PY - 2023/7
Y1 - 2023/7
N2 - 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.
AB - 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.
KW - brevundimonas diminuta
KW - culture negative
KW - keratitis
KW - Metagenomics
UR - http://www.scopus.com/inward/record.url?scp=85146512491&partnerID=8YFLogxK
U2 - 10.1177/11206721221149077
DO - 10.1177/11206721221149077
M3 - Article
C2 - 36617769
AN - SCOPUS:85146512491
SN - 1120-6721
VL - 33
SP - 1589
EP - 1595
JO - European Journal of Ophthalmology
JF - European Journal of Ophthalmology
IS - 4
ER -