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High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

The rise of antimicrobial-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men wit...

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Autores principales: Sanderson, Nicholas D., Swann, Jeremy, Barker, Leanne, Kavanagh, James, Hoosdally, Sarah, Crook, Derrick, Street, Teresa L., Eyre, David W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545138/
https://www.ncbi.nlm.nih.gov/pubmed/32873606
http://dx.doi.org/10.1101/gr.262865.120
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author Sanderson, Nicholas D.
Swann, Jeremy
Barker, Leanne
Kavanagh, James
Hoosdally, Sarah
Crook, Derrick
Street, Teresa L.
Eyre, David W.
author_facet Sanderson, Nicholas D.
Swann, Jeremy
Barker, Leanne
Kavanagh, James
Hoosdally, Sarah
Crook, Derrick
Street, Teresa L.
Eyre, David W.
author_sort Sanderson, Nicholas D.
collection PubMed
description The rise of antimicrobial-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge. Here, we show an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20× reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection.
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spelling pubmed-75451382020-10-19 High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing Sanderson, Nicholas D. Swann, Jeremy Barker, Leanne Kavanagh, James Hoosdally, Sarah Crook, Derrick Street, Teresa L. Eyre, David W. Genome Res Method The rise of antimicrobial-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge. Here, we show an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20× reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection. Cold Spring Harbor Laboratory Press 2020-09 /pmc/articles/PMC7545138/ /pubmed/32873606 http://dx.doi.org/10.1101/gr.262865.120 Text en © 2020 Sanderson et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Method
Sanderson, Nicholas D.
Swann, Jeremy
Barker, Leanne
Kavanagh, James
Hoosdally, Sarah
Crook, Derrick
Street, Teresa L.
Eyre, David W.
High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
title High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
title_full High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
title_fullStr High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
title_full_unstemmed High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
title_short High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
title_sort high precision neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545138/
https://www.ncbi.nlm.nih.gov/pubmed/32873606
http://dx.doi.org/10.1101/gr.262865.120
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