Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform

the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT); Liying Low; Kenji Nakamichi; Lakshmi Akileswaran; Cecilia S. Lee; Aaron Y. Lee; George Moussa; Phil Murray; Graham Wallace; Russell N. Van Gelder; Saaeha Rauz

doi:10.1016/j.ajo.2022.05.022

Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform

the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT), Liying Low, Kenji Nakamichi, Lakshmi Akileswaran, Cecilia S. Lee, Aaron Y. Lee, George Moussa, Phil Murray, Graham Wallace, Russell N. Van Gelder, Saaeha Rauz^*

^*Corresponding author for this work

Inflammation and Ageing

Research output: Contribution to journal › Article › peer-review

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Abstract

Purpose
To evaluate the utility of nanopore sequencing for identifying 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).

Design
Cross-sectional diagnostic comparison.

Methods
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.

Results
Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively.

Conclusions
Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting 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.

Original language	English
Pages (from-to)	243-251
Number of pages	9
Journal	American Journal of Ophthalmology
Volume	242
Early online date	30 May 2022
DOIs	https://doi.org/10.1016/j.ajo.2022.05.022
Publication status	E-pub ahead of print - 30 May 2022

Bibliographical note

Funding Information:
Funding/support: This study was funded through the Royal College of Ophthalmologists and Fight for Sight Ophthalmology Trainee Research Network Award ( Ref. 24 CO3), the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC)/Royal Centre for Defence Medicine, Ministry of Defence (UK) grant (Ref. RCDM—ADMST0003: ‘Rapid Diagnosis of Corneal Infections’), and the Sandwell and West Birmingham Hospitals 2021 Ophthalmology Research and Development fund. Dr Liying Low was funded by a Fight for Sight Clinical Research Fellowship (Ref. 1840/41) and is a recipient of the National Institute for Health Research (NIHR) Clinical Lectureship. Dr Cecilia Lee is supported by an National Institutes of Health (NIH) Research Career Development Award (Ref. K23EY02492). Dr Aaron Lee is supported by grants from the NIH/National Eye Institute (NEI) Research Career Development Award (Ref. K23EY029246), National Institute on Ageing (NIA)/NIH (Ref. U19AG066567) and Research to Prevent Blindness, Alcon Research Institute, and Latham Vision Funds. Professor Russell N Van Gelder is supported by an unrestricted grant from Research to Prevent Blindness and the Mark J. Daily, MD Research Fund. Miss Saaeha Rauz is supported by the Medical Research Council Developmental Pathway Funding Scheme “Development of a synthetic biomembrane dressing that prevents corneal scarring” (Ref. MR/N019016/1). Financial disclosures: Dr Aaron Lee has received grants/contracts from Lowy Medical Research Institute, Carl Zeiss Meditec, Microsoft, and Santen with payments made to the University of Washington, Seattle. Dr Aaron Lee has received payments or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Bascom Palmer Eye Institute, Harvard Children's Hospital, iVista Medical Education, Inc, Topcon and Tufts Medical Center. Dr Aaron Lee has leadership roles in the Collaborative Community on Ophthalmic Imaging (unpaid member of the Executive Committee), and American Academy of Ophthalmology (unpaid chair of Information Technology). Dr Aaron Lee has received payments from the University of Washington (Latham Vision Research Innovation Award), US Food and Drug Administration, and Verana Health. Professor Philip I. Murray receives royalties from the Oxford University Press (Oxford Handbook of Ophthalmology 4 th Edition), and has received payment or honoraria for presentation from Scope Eyecare. All authors attest that they meet the current ICMJE criteria for authorship. Other acknowledgements: We would like to thank Angela F. Sandt, Radoslaw Poplawski, and Zahira Maqsood for their contribution to this project. Dr Cecilia Lee is supported by grants from the National Eye Institute (NEI) Research Career Development Award (Ref. K23EY02492), National Institute on Ageing (NIA) (Ref. R01AG060942, U19AG066567) and Latham Vision Funds.

Funding Information:
Funding/support: This study was funded through the Royal College of Ophthalmologists and Fight for Sight Ophthalmology Trainee Research Network Award (Ref. 24CO3), the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC)/Royal Centre for Defence Medicine, Ministry of Defence (UK) grant (Ref. RCDM—ADMST0003: ‘Rapid Diagnosis of Corneal Infections’), and the Sandwell and West Birmingham Hospitals 2021 Ophthalmology Research and Development fund. Dr Liying Low was funded by a Fight for Sight Clinical Research Fellowship (Ref. 1840/41) and is a recipient of the National Institute for Health Research (NIHR) Clinical Lectureship. Dr Cecilia Lee is supported by an National Institutes of Health (NIH) Research Career Development Award (Ref. K23EY02492). Dr Aaron Lee is supported by grants from the NIH/National Eye Institute (NEI) Research Career Development Award (Ref. K23EY029246), National Institute on Ageing (NIA)/NIH (Ref. U19AG066567) and Research to Prevent Blindness, Alcon Research Institute, and Latham Vision Funds. Professor Russell N Van Gelder is supported by an unrestricted grant from Research to Prevent Blindness and the Mark J. Daily, MD Research Fund. Miss Saaeha Rauz is supported by the Medical Research Council Developmental Pathway Funding Scheme “Development of a synthetic biomembrane dressing that prevents corneal scarring” (Ref. MR/N019016/1). Financial disclosures: Dr Aaron Lee has received grants/contracts from Lowy Medical Research Institute, Carl Zeiss Meditec, Microsoft, and Santen with payments made to the University of Washington, Seattle. Dr Aaron Lee has received payments or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Bascom Palmer Eye Institute, Harvard Children's Hospital, iVista Medical Education, Inc, Topcon and Tufts Medical Center. Dr Aaron Lee has leadership roles in the Collaborative Community on Ophthalmic Imaging (unpaid member of the Executive Committee), and American Academy of Ophthalmology (unpaid chair of Information Technology). Dr Aaron Lee has received payments from the University of Washington (Latham Vision Research Innovation Award), US Food and Drug Administration, and Verana Health. Professor Philip I. Murray receives royalties from the Oxford University Press (Oxford Handbook of Ophthalmology 4th Edition), and has received payment or honoraria for presentation from Scope Eyecare. All authors attest that they meet the current ICMJE criteria for authorship. Other acknowledgements: We would like to thank Angela F. Sandt, Radoslaw Poplawski, and Zahira Maqsood for their contribution to this project. Dr Cecilia Lee is supported by grants from the National Eye Institute (NEI) Research Career Development Award (Ref. K23EY02492), National Institute on Ageing (NIA) (Ref. R01AG060942, U19AG066567) and Latham Vision Funds. The West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT) collaborators: George Moussa, Pavitra Garala, Li Jiang, Sam Yuen Sum Lee, Ian de Silva, Aaron Ng, William Fusi-Rubiano, Yu Jeat Chong, Jesse Panthagani, Xiao Li Chen, Maninee Purohit, Hetvi Bhatt, Hemalatha Kolli, Usama Kanj, Richard Blanch, and Sreekanth Sreekantam. Data Availability: Data are available upon request.

Publisher Copyright:
© 2022 The Authors

Keywords

Eye infection
Sequencing
Endophthalmitis
Nanopore sequencing
16S rRNA
Whole Genome Sequencing

ASJC Scopus subject areas

Ophthalmology

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10.1016/j.ajo.2022.05.022Licence: Creative Commons: Attribution (CC BY)

LowL2022DeepFinal published version, 367 KBLicence: Creative Commons: Attribution (CC BY)

Development of a synthetic flowable dressing that prevents corneal scarring
Rauz, S., Spyropoulos, F., Barnes, N., Billingham, L., Wallace, G., Grover, L. & Logan, A.
Medical Research Council
1/08/16 → 30/09/23
Project: Research Councils

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the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT), Low, L., Nakamichi, K., Akileswaran, L., Lee, C. S., Lee, A. Y., Moussa, G., Murray, P., Wallace, G., Van Gelder, R. N., & Rauz, S. (2022). Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform. American Journal of Ophthalmology, 242, 243-251. Advance online publication. https://doi.org/10.1016/j.ajo.2022.05.022

@article{38b5747cc4f5461285df5f9b3da70f01,

title = "Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform",

abstract = "Purpose To evaluate the utility of nanopore sequencing for identifying 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). Design Cross-sectional diagnostic comparison. Methods 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. Results Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively. Conclusions Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting 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.",

keywords = "Eye infection, Sequencing, Endophthalmitis, Nanopore sequencing, 16S rRNA, Whole Genome Sequencing",

author = "{the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT)} and Liying Low and Kenji Nakamichi and Lakshmi Akileswaran and Lee, {Cecilia S.} and Lee, {Aaron Y.} and George Moussa and Phil Murray and Graham Wallace and {Van Gelder}, {Russell N.} and Saaeha Rauz",

note = "Funding Information: Funding/support: This study was funded through the Royal College of Ophthalmologists and Fight for Sight Ophthalmology Trainee Research Network Award ( Ref. 24 CO3), the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC)/Royal Centre for Defence Medicine, Ministry of Defence (UK) grant (Ref. RCDM—ADMST0003: {\textquoteleft}Rapid Diagnosis of Corneal Infections{\textquoteright}), and the Sandwell and West Birmingham Hospitals 2021 Ophthalmology Research and Development fund. Dr Liying Low was funded by a Fight for Sight Clinical Research Fellowship (Ref. 1840/41) and is a recipient of the National Institute for Health Research (NIHR) Clinical Lectureship. Dr Cecilia Lee is supported by an National Institutes of Health (NIH) Research Career Development Award (Ref. K23EY02492). Dr Aaron Lee is supported by grants from the NIH/National Eye Institute (NEI) Research Career Development Award (Ref. K23EY029246), National Institute on Ageing (NIA)/NIH (Ref. U19AG066567) and Research to Prevent Blindness, Alcon Research Institute, and Latham Vision Funds. Professor Russell N Van Gelder is supported by an unrestricted grant from Research to Prevent Blindness and the Mark J. Daily, MD Research Fund. Miss Saaeha Rauz is supported by the Medical Research Council Developmental Pathway Funding Scheme “Development of a synthetic biomembrane dressing that prevents corneal scarring” (Ref. MR/N019016/1). Financial disclosures: Dr Aaron Lee has received grants/contracts from Lowy Medical Research Institute, Carl Zeiss Meditec, Microsoft, and Santen with payments made to the University of Washington, Seattle. Dr Aaron Lee has received payments or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Bascom Palmer Eye Institute, Harvard Children's Hospital, iVista Medical Education, Inc, Topcon and Tufts Medical Center. Dr Aaron Lee has leadership roles in the Collaborative Community on Ophthalmic Imaging (unpaid member of the Executive Committee), and American Academy of Ophthalmology (unpaid chair of Information Technology). Dr Aaron Lee has received payments from the University of Washington (Latham Vision Research Innovation Award), US Food and Drug Administration, and Verana Health. Professor Philip I. Murray receives royalties from the Oxford University Press (Oxford Handbook of Ophthalmology 4 th Edition), and has received payment or honoraria for presentation from Scope Eyecare. All authors attest that they meet the current ICMJE criteria for authorship. Other acknowledgements: We would like to thank Angela F. Sandt, Radoslaw Poplawski, and Zahira Maqsood for their contribution to this project. Dr Cecilia Lee is supported by grants from the National Eye Institute (NEI) Research Career Development Award (Ref. K23EY02492), National Institute on Ageing (NIA) (Ref. R01AG060942, U19AG066567) and Latham Vision Funds. Funding Information: Funding/support: This study was funded through the Royal College of Ophthalmologists and Fight for Sight Ophthalmology Trainee Research Network Award (Ref. 24CO3), the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC)/Royal Centre for Defence Medicine, Ministry of Defence (UK) grant (Ref. RCDM—ADMST0003: {\textquoteleft}Rapid Diagnosis of Corneal Infections{\textquoteright}), and the Sandwell and West Birmingham Hospitals 2021 Ophthalmology Research and Development fund. Dr Liying Low was funded by a Fight for Sight Clinical Research Fellowship (Ref. 1840/41) and is a recipient of the National Institute for Health Research (NIHR) Clinical Lectureship. Dr Cecilia Lee is supported by an National Institutes of Health (NIH) Research Career Development Award (Ref. K23EY02492). Dr Aaron Lee is supported by grants from the NIH/National Eye Institute (NEI) Research Career Development Award (Ref. K23EY029246), National Institute on Ageing (NIA)/NIH (Ref. U19AG066567) and Research to Prevent Blindness, Alcon Research Institute, and Latham Vision Funds. Professor Russell N Van Gelder is supported by an unrestricted grant from Research to Prevent Blindness and the Mark J. Daily, MD Research Fund. Miss Saaeha Rauz is supported by the Medical Research Council Developmental Pathway Funding Scheme “Development of a synthetic biomembrane dressing that prevents corneal scarring” (Ref. MR/N019016/1). Financial disclosures: Dr Aaron Lee has received grants/contracts from Lowy Medical Research Institute, Carl Zeiss Meditec, Microsoft, and Santen with payments made to the University of Washington, Seattle. Dr Aaron Lee has received payments or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Bascom Palmer Eye Institute, Harvard Children's Hospital, iVista Medical Education, Inc, Topcon and Tufts Medical Center. Dr Aaron Lee has leadership roles in the Collaborative Community on Ophthalmic Imaging (unpaid member of the Executive Committee), and American Academy of Ophthalmology (unpaid chair of Information Technology). Dr Aaron Lee has received payments from the University of Washington (Latham Vision Research Innovation Award), US Food and Drug Administration, and Verana Health. Professor Philip I. Murray receives royalties from the Oxford University Press (Oxford Handbook of Ophthalmology 4th Edition), and has received payment or honoraria for presentation from Scope Eyecare. All authors attest that they meet the current ICMJE criteria for authorship. Other acknowledgements: We would like to thank Angela F. Sandt, Radoslaw Poplawski, and Zahira Maqsood for their contribution to this project. Dr Cecilia Lee is supported by grants from the National Eye Institute (NEI) Research Career Development Award (Ref. K23EY02492), National Institute on Ageing (NIA) (Ref. R01AG060942, U19AG066567) and Latham Vision Funds. The West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT) collaborators: George Moussa, Pavitra Garala, Li Jiang, Sam Yuen Sum Lee, Ian de Silva, Aaron Ng, William Fusi-Rubiano, Yu Jeat Chong, Jesse Panthagani, Xiao Li Chen, Maninee Purohit, Hetvi Bhatt, Hemalatha Kolli, Usama Kanj, Richard Blanch, and Sreekanth Sreekantam. Data Availability: Data are available upon request. Publisher Copyright: {\textcopyright} 2022 The Authors",

year = "2022",

month = may,

day = "30",

doi = "10.1016/j.ajo.2022.05.022",

language = "English",

volume = "242",

pages = "243--251",

journal = "American Journal of Ophthalmology",

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the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT), Low, L, Nakamichi, K, Akileswaran, L, Lee, CS, Lee, AY, Moussa, G, Murray, P , Wallace, G, Van Gelder, RN & Rauz, S 2022, 'Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform', American Journal of Ophthalmology, vol. 242, pp. 243-251. https://doi.org/10.1016/j.ajo.2022.05.022

Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform. / the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT) ; Low, Liying; Nakamichi, Kenji et al.
In: American Journal of Ophthalmology, Vol. 242, 30.05.2022, p. 243-251.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform

AU - the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT)

AU - Low, Liying

AU - Nakamichi, Kenji

AU - Akileswaran, Lakshmi

AU - Lee, Cecilia S.

AU - Lee, Aaron Y.

AU - Moussa, George

AU - Murray, Phil

AU - Wallace, Graham

AU - Van Gelder, Russell N.

AU - Rauz, Saaeha

N1 - Funding Information: Funding/support: This study was funded through the Royal College of Ophthalmologists and Fight for Sight Ophthalmology Trainee Research Network Award ( Ref. 24 CO3), the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC)/Royal Centre for Defence Medicine, Ministry of Defence (UK) grant (Ref. RCDM—ADMST0003: ‘Rapid Diagnosis of Corneal Infections’), and the Sandwell and West Birmingham Hospitals 2021 Ophthalmology Research and Development fund. Dr Liying Low was funded by a Fight for Sight Clinical Research Fellowship (Ref. 1840/41) and is a recipient of the National Institute for Health Research (NIHR) Clinical Lectureship. Dr Cecilia Lee is supported by an National Institutes of Health (NIH) Research Career Development Award (Ref. K23EY02492). Dr Aaron Lee is supported by grants from the NIH/National Eye Institute (NEI) Research Career Development Award (Ref. K23EY029246), National Institute on Ageing (NIA)/NIH (Ref. U19AG066567) and Research to Prevent Blindness, Alcon Research Institute, and Latham Vision Funds. Professor Russell N Van Gelder is supported by an unrestricted grant from Research to Prevent Blindness and the Mark J. Daily, MD Research Fund. Miss Saaeha Rauz is supported by the Medical Research Council Developmental Pathway Funding Scheme “Development of a synthetic biomembrane dressing that prevents corneal scarring” (Ref. MR/N019016/1). Financial disclosures: Dr Aaron Lee has received grants/contracts from Lowy Medical Research Institute, Carl Zeiss Meditec, Microsoft, and Santen with payments made to the University of Washington, Seattle. Dr Aaron Lee has received payments or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Bascom Palmer Eye Institute, Harvard Children's Hospital, iVista Medical Education, Inc, Topcon and Tufts Medical Center. Dr Aaron Lee has leadership roles in the Collaborative Community on Ophthalmic Imaging (unpaid member of the Executive Committee), and American Academy of Ophthalmology (unpaid chair of Information Technology). Dr Aaron Lee has received payments from the University of Washington (Latham Vision Research Innovation Award), US Food and Drug Administration, and Verana Health. Professor Philip I. Murray receives royalties from the Oxford University Press (Oxford Handbook of Ophthalmology 4 th Edition), and has received payment or honoraria for presentation from Scope Eyecare. All authors attest that they meet the current ICMJE criteria for authorship. Other acknowledgements: We would like to thank Angela F. Sandt, Radoslaw Poplawski, and Zahira Maqsood for their contribution to this project. Dr Cecilia Lee is supported by grants from the National Eye Institute (NEI) Research Career Development Award (Ref. K23EY02492), National Institute on Ageing (NIA) (Ref. R01AG060942, U19AG066567) and Latham Vision Funds. Funding Information: Funding/support: This study was funded through the Royal College of Ophthalmologists and Fight for Sight Ophthalmology Trainee Research Network Award (Ref. 24CO3), the National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre (SRMRC)/Royal Centre for Defence Medicine, Ministry of Defence (UK) grant (Ref. RCDM—ADMST0003: ‘Rapid Diagnosis of Corneal Infections’), and the Sandwell and West Birmingham Hospitals 2021 Ophthalmology Research and Development fund. Dr Liying Low was funded by a Fight for Sight Clinical Research Fellowship (Ref. 1840/41) and is a recipient of the National Institute for Health Research (NIHR) Clinical Lectureship. Dr Cecilia Lee is supported by an National Institutes of Health (NIH) Research Career Development Award (Ref. K23EY02492). Dr Aaron Lee is supported by grants from the NIH/National Eye Institute (NEI) Research Career Development Award (Ref. K23EY029246), National Institute on Ageing (NIA)/NIH (Ref. U19AG066567) and Research to Prevent Blindness, Alcon Research Institute, and Latham Vision Funds. Professor Russell N Van Gelder is supported by an unrestricted grant from Research to Prevent Blindness and the Mark J. Daily, MD Research Fund. Miss Saaeha Rauz is supported by the Medical Research Council Developmental Pathway Funding Scheme “Development of a synthetic biomembrane dressing that prevents corneal scarring” (Ref. MR/N019016/1). Financial disclosures: Dr Aaron Lee has received grants/contracts from Lowy Medical Research Institute, Carl Zeiss Meditec, Microsoft, and Santen with payments made to the University of Washington, Seattle. Dr Aaron Lee has received payments or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Bascom Palmer Eye Institute, Harvard Children's Hospital, iVista Medical Education, Inc, Topcon and Tufts Medical Center. Dr Aaron Lee has leadership roles in the Collaborative Community on Ophthalmic Imaging (unpaid member of the Executive Committee), and American Academy of Ophthalmology (unpaid chair of Information Technology). Dr Aaron Lee has received payments from the University of Washington (Latham Vision Research Innovation Award), US Food and Drug Administration, and Verana Health. Professor Philip I. Murray receives royalties from the Oxford University Press (Oxford Handbook of Ophthalmology 4th Edition), and has received payment or honoraria for presentation from Scope Eyecare. All authors attest that they meet the current ICMJE criteria for authorship. Other acknowledgements: We would like to thank Angela F. Sandt, Radoslaw Poplawski, and Zahira Maqsood for their contribution to this project. Dr Cecilia Lee is supported by grants from the National Eye Institute (NEI) Research Career Development Award (Ref. K23EY02492), National Institute on Ageing (NIA) (Ref. R01AG060942, U19AG066567) and Latham Vision Funds. The West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT) collaborators: George Moussa, Pavitra Garala, Li Jiang, Sam Yuen Sum Lee, Ian de Silva, Aaron Ng, William Fusi-Rubiano, Yu Jeat Chong, Jesse Panthagani, Xiao Li Chen, Maninee Purohit, Hetvi Bhatt, Hemalatha Kolli, Usama Kanj, Richard Blanch, and Sreekanth Sreekantam. Data Availability: Data are available upon request. Publisher Copyright: © 2022 The Authors

PY - 2022/5/30

Y1 - 2022/5/30

N2 - Purpose To evaluate the utility of nanopore sequencing for identifying 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). Design Cross-sectional diagnostic comparison. Methods 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. Results Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively. Conclusions Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting 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.

AB - Purpose To evaluate the utility of nanopore sequencing for identifying 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). Design Cross-sectional diagnostic comparison. Methods 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. Results Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively. Conclusions Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting 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.

KW - Eye infection

KW - Sequencing

KW - Endophthalmitis

KW - Nanopore sequencing

KW - 16S rRNA

KW - Whole Genome Sequencing

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U2 - 10.1016/j.ajo.2022.05.022

DO - 10.1016/j.ajo.2022.05.022

M3 - Article

C2 - 35660421

SN - 0002-9394

VL - 242

SP - 243

EP - 251

JO - American Journal of Ophthalmology

JF - American Journal of Ophthalmology

ER -

the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT), Low L, Nakamichi K, Akileswaran L, Lee CS, Lee AY et al. Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform. American Journal of Ophthalmology. 2022 May 30;242:243-251. Epub 2022 May 30. doi: 10.1016/j.ajo.2022.05.022

Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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Projects

Development of a synthetic flowable dressing that prevents corneal scarring

Cite this