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Rocha-de-Lossada C, Mazzotta C, Gabrielli F, Papa FT, Gómez-Huertas C, García-López C, Urbinati F, Rachwani-Anil R, García-Lorente M, Sánchez-González JM, Rechichi M, Rubegni G, Borroni D. Ocular Surface Microbiota in Naïve Keratoconus: A Multicenter Validation Study. J Clin Med 2023; 12:6354. [PMID: 37834997 PMCID: PMC10573816 DOI: 10.3390/jcm12196354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of Ophthalmology, the mNGS 16S rRNA sequencing method of studying the microbiota and ocular microbiome is gaining more and more weight in the scientific community. This study aims to characterize the ocular microbiota of patients diagnosed with keratoconus who have not undergone any prior surgical treatment using the mNGS 16S rRNA sequencing method. Samples of naïve keratoconus patients were collected with an eNAT with 1 mL of Liquid Amies Medium (Copan Brescia, Italy), and DNA was extracted and analyzed with 16S NGS. The microbiota analysis showed a relative abundance of microorganisms at the phylum level in each sample collected from 38 patients with KC and 167 healthy controls. A comparison between healthy control and keratoconus samples identified two genera unique to keratoconus, Pelomonas and Ralstonia. Our findings suggest that alterations in the microbiota may play a role in the complex scenario of KC development.
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Affiliation(s)
- Carlos Rocha-de-Lossada
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
- Ophthalmology Department, QVision, Vithas Almería, 04120 Almeria, Spain
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | - Cosimo Mazzotta
- Siena Crosslinking Center, 53100 Siena, Italy;
- Departmental Ophthalmology Unit, USL Toscana Sud Est l, 53100 Siena, Italy
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Federico Gabrielli
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Filomena Tiziana Papa
- Biolab SRL, Laboratorio di Genetica e Genomica Molecolare, Largo degli Aranci, 9, 63100 Ascoli Piceno, Italy; (F.G.); (F.T.P.)
| | - Carmen Gómez-Huertas
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Celia García-López
- Department of Ophthalmology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain; (C.G.-H.); (C.G.-L.)
| | - Facundo Urbinati
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - María García-Lorente
- Ophthalmology Department, Hospital Regional Universitario Málaga, 29010 Malaga, Spain; (F.U.); (M.G.-L.)
| | | | - Miguel Rechichi
- Centro Polispecialistico Mediterraneo, 88050 Sellia Marina, Italy;
| | - Giovanni Rubegni
- Postgraduate Ophthalmology School, University of Siena, 53100 Siena, Italy;
| | - Davide Borroni
- Eyemetagenomics Ltd., 71–75, Shelton Street, Covent Garden, London WC2H 9JQ, UK;
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Borroni D, Bonzano C, Sánchez-González JM, Rachwani-Anil R, Zamorano-Martín F, Pereza-Nieves J, Traverso CE, García Lorente M, Rodríguez-Calvo-de-Mora M, Esposito A, Godin F, Rocha-de-Lossada C. Shotgun metagenomic sequencing in culture negative microbial keratitis. Eur J Ophthalmol 2023:11206721221149077. [PMID: 36617769 DOI: 10.1177/11206721221149077] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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 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.
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Affiliation(s)
- Davide Borroni
- Department of Ophthalmology, Riga Stradins University, Riga, Latvia
| | - Chiara Bonzano
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | | | | | - Carlo Enrico Traverso
- DiNOGMI, University of Genoa and IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | | | | | - Alfonso Esposito
- 18470International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fernando Godin
- Department of Ophthalmology, Universidad El Bosque, Bogotá, Colombia
| | - Carlos Rocha-de-Lossada
- Qvision, Opththalmology Department, VITHAS Almería Hospital, Almería, Spain.,Ophthalmology Department, VITHAS Málaga, Málaga, Spain.,Hospital Regional Universitario de Málaga, Plaza del Hospital Civil, Málaga, Spain.,Departamento de Cirugía, Universidad de Sevilla, Área de Oftalmología, Doctor Fedriani, Seville, Spain
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Borroni D. Granulicatella Adiacens as an Unusual Cause of Microbial Keratitis: A Metagenomic Approach. Ocul Immunol Inflamm 2021; 30:1550-1551. [PMID: 34236294 DOI: 10.1080/09273948.2021.1933066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Metagenomics Next-Generation Sequencing can provide taxonomic and functional profiles of microbial keratitis communities without the need to culture infected corneal samples. We share our experience on a case with negative culture but positive metagenomic results.
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Affiliation(s)
- Davide Borroni
- The Veneto Eye Bank Foundation, Venice, Italy.,Department of Ophthalmology, Riga Stradins University, Riga, Latvia
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Borroni D, Rachwani-Anil R, González JMS, Rodríguez-Calvo-de-Mora M, Rocha de Lossada C. Metagenome techniques to reduce diagnostic delay in Acanthamoeba keratitis. Rom J Ophthalmol 2021; 65:307-308. [PMID: 35036659 PMCID: PMC8697792 DOI: 10.22336/rjo.2021.63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 01/08/2023] Open
Affiliation(s)
- Davide Borroni
- The Veneto Eye Bank Foundation, Venice, Italy.,Department of Doctoral Studies, Riga Stradins University, Riga, Latvia
| | - Rahul Rachwani-Anil
- Department of Ophthalmology, Regional University Hospital of Malaga, Malaga, Spain
| | - José María Sánchez González
- Department of Physics of Condensed Matter, University of Seville, Seville, Spain.,Department of Ophthalmology (Tecnolaser Clinic Vision®), Seville, Spain
| | | | - Carlos Rocha de Lossada
- Department of Ophthalmology (Qvision), VITHAS Hospital, Almería, Spain; Department of Ophthalmology, Hospital Virgen de las Nieves, Granada, Spain; Department of Ophthalmology, Ceuta Medical Center, Ceuta, Spain
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