Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.
Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.
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DOI：
10.1016/j.ajo.2022.05.022
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发表时间：
2022-10
影响因子：
4.2
通讯作者：
Rauz, Saaeha
中科院分区：
文献类型：
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作者：
Low, Liying;Nakamichi, Kenji;Akileswaran, Lakshmi;Lee, Cecilia S.;Lee, Aaron Y.;Moussa, George;Murray, Philip, I;Wallace, Graham R.;Van Gelder, Russell N.;Rauz, Saaeha
To evaluate the utility of nanopore sequencing for identification of potential causative pathogens in endophthalmitis, comparing culture results against full-length 16S rRNA nanopore sequencing (16S Nanopore), whole genome nanopore sequencing (Nanopore WGS) and Illumina (Illumina WGS) Cross-sectional diagnostic comparison Patients with clinically suspected endophthalmitis underwent intraocular vitreous biopsy as per standard-care. Clinical samples were cultured by conventional methods, together with full length 16S rRNA and WGS using nanopore and Illumina sequencing platforms. Of twenty-three patients (median age 68.5[range 47–88] years; 14[61%] male), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism as in all of the culture-positive cases and identified potential pathogens in 2(40%) of culture-negative cases. Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreement at genus level between culture and 16S Nanopore, Nanopore WGS and Illumina WGS were 75%, 100% and 78% respectively. WGS has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detection of potential pathogens in endophthalmitis. Moreover, WGS has the ability to detect other potential pathogens in culture-negative cases. Whilst Nanopore and Illumina WGS provide comparable data, nanopore sequencing provides potential for cost-effective point-of-care diagnostics. Nanopore sequencing detected the cultured organism in all (18/18) of the culture-positive endophthalmitis cases and identified potential pathogens in 40% (2/5) of culture-negative cases. Whole genome nanopore sequencing had higher sensitivity than 16S sequencing and was comparable to Illumina whole genome sequencing.
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影响因子：
4.1
作者：
Jun, Kang Il;Oh, Baek-Lok;Moon, Jangsup
通讯作者：
Moon, Jangsup
影响因子：
4
作者：
通讯作者：
--
影响因子：
4.2
作者：
Lee CS;Hong B;Kasi SK;Aderman C;Talcott KE;Adam MK;Yue B;Akileswaran L;Nakamichi K;Wu Y;Rezaei KA;Olmos de Koo LC;Chee YE;Lee AY;Garg SJ;Van Gelder RN;Endophthalmitis Study Group
通讯作者：
Endophthalmitis Study Group
影响因子：
4.4
作者：
Doan T;Akileswaran L;Andersen D;Johnson B;Ko N;Shrestha A;Shestopalov V;Lee CS;Lee AY;Van Gelder RN
通讯作者：
Van Gelder RN
影响因子：
46.9
作者：
Jain M;Koren S;Miga KH;Quick J;Rand AC;Sasani TA;Tyson JR;Beggs AD;Dilthey AT;Fiddes IT;Malla S;Marriott H;Nieto T;O'Grady J;Olsen HE;Pedersen BS;Rhie A;Richardson H;Quinlan AR;Snutch TP;Tee L;Paten B;Phillippy AM;Simpson JT;Loman NJ;Loose M
通讯作者：
Loose M