New insights into culture negative endophthalmitis by unbiased next generation sequencing
| Autor: | Rajagopalaboopathi Jayasudha, Sisinthy Shivaji, Savitri Sharma, Bhavani Sontam, Joveeta Joseph, Moumita Chakrabarti, Kalyana C. Sama, Raja Narayanan, Mudit Tyagi, Dhanshree Deshmukh |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Adult Male Adolescent Biopsy lcsh:Medicine Biology medicine.disease_cause Proof of Concept Study DNA sequencing Article law.invention Microbiology 03 medical and health sciences 0302 clinical medicine Endophthalmitis law RNA Ribosomal 16S Haemophilus medicine Humans lcsh:Science Child Polymerase chain reaction Aged Multidisciplinary Bacteria Streptococcus lcsh:R Fungi High-Throughput Nucleotide Sequencing Infant Middle Aged medicine.disease biology.organism_classification DNA extraction 030104 developmental biology Child Preschool Gemella lcsh:Q Female Staphylococcus 030217 neurology & neurosurgery |
| Zdroj: | Scientific Reports Scientific Reports, Vol 9, Iss 1, Pp 1-10 (2019) |
| ISSN: | 2045-2322 |
| Popis: | The proof-of-concept, study to investigate the presence of microorganisms in presumed infectious endophthalmitis using Next generation sequencing (NGS) was carried out in vitreous biopsies from 34 patients with endophthalmitis, and thirty patients undergoing surgery for non-infectious retinal disorders as controls. Following DNA extraction using the Qiagen mini kit and PCR amplification of the V3–V4 regions of the bacterial 16S rRNA and ITS 2 region of fungus, they samples were sequenced on an Illumina HiSeq 2500 Machine. Paired reads were curated, taxonomically labeled, and filtered. Culture based diagnosis was achieved in 15/34 (44%) patients while NGS diagnosed the presence of microbes in 30/34 (88%) patients (bacteria in 26/30, fungi in 2/30, mixed infections in 2/30 cases). All 30 controls were negative for bacteria or fungus by NGS. There was good agreement between culture and NGS for culture-positive cases. Among culture negative cases, DNA of common culturable bacteria were identified like Streptococcus sp., Staphylococcus sp., Pseudomonas sp., Gemella sp., Haemophilus sp., Acinetobacter sp. The specificity of NGS with culture and clinical diagnosis was found to be 20% and 100% respectively and sensitivity of NGS with culture and clinical diagnosis was found to be 87.5% and 88% respectively. NGS appears to be promising diagnostic platform for the diagnosis of infectious culture negative endophthalmitis. |
| Databáze: | OpenAIRE |
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