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Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples

Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non-targeted sequencing approach with rapid and precise characte...

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Autores principales: Butt, Salman L., Kariithi, Henry M., Volkening, Jeremy D., Taylor, Tonya L., Leyson, Christina, Pantin-Jackwood, Mary, Suarez, David L., Stanton, James B., Afonso, Claudio L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751482/
https://www.ncbi.nlm.nih.gov/pubmed/36532355
http://dx.doi.org/10.3389/fvets.2022.1073919
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author Butt, Salman L.
Kariithi, Henry M.
Volkening, Jeremy D.
Taylor, Tonya L.
Leyson, Christina
Pantin-Jackwood, Mary
Suarez, David L.
Stanton, James B.
Afonso, Claudio L.
author_facet Butt, Salman L.
Kariithi, Henry M.
Volkening, Jeremy D.
Taylor, Tonya L.
Leyson, Christina
Pantin-Jackwood, Mary
Suarez, David L.
Stanton, James B.
Afonso, Claudio L.
author_sort Butt, Salman L.
collection PubMed
description Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non-targeted sequencing approach with rapid and precise characterization of pathogens should help respiratory disease management by providing a comprehensive view of the causes of disease. Long-read portable sequencers have significant potential advantages over established short-read sequencers due to portability, speed, and lower cost. The applicability of short reads random sequencing for direct detection of pathogens in clinical poultry samples has been previously demonstrated. Here we demonstrate the feasibility of long read random sequencing approaches to identify disease agents in clinical samples. Experimental oropharyngeal swab samples (n = 12) from chickens infected with infectious bronchitis virus (IBV), avian influenza virus (AIV) and Mycoplasma synoviae (MS) and field-collected clinical oropharyngeal swab samples (n = 11) from Kenyan live bird markets previously testing positive for Newcastle disease virus (NDV) were randomly sequenced on the MinION platform and results validated by comparing to real time PCR and short read random sequencing in the Illumina MiSeq platform. In the swabs from experimental infections, each of three agents in every RT-qPCR-positive sample (Ct range 19–34) was detectable within 1 h on the MinION platform, except for AIV one agent in one sample (Ct = 36.21). Nine of 12 IBV-positive samples were assigned genotypes within 1 h, as were five of 11 AIV-positive samples. MinION relative abundances of the test agent (AIV, IBV and MS) were highly correlated with RT-qPCR Ct values (R range−0.82 to−0.98). In field-collected clinical swab samples, NDV (Ct range 12–37) was detected in all eleven samples within 1 h of MinION sequencing, with 10 of 11 samples accurately genotyped within 1 h. All NDV-positive field samples were found to be co-infected with one or more additional respiratory agents. These results demonstrate that MinION sequencing can provide rapid, and sensitive non-targeted detection and genetic characterization of co-existing respiratory pathogens in clinical samples with similar performance to the Illumina MiSeq.
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spelling pubmed-97514822022-12-16 Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples Butt, Salman L. Kariithi, Henry M. Volkening, Jeremy D. Taylor, Tonya L. Leyson, Christina Pantin-Jackwood, Mary Suarez, David L. Stanton, James B. Afonso, Claudio L. Front Vet Sci Veterinary Science Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non-targeted sequencing approach with rapid and precise characterization of pathogens should help respiratory disease management by providing a comprehensive view of the causes of disease. Long-read portable sequencers have significant potential advantages over established short-read sequencers due to portability, speed, and lower cost. The applicability of short reads random sequencing for direct detection of pathogens in clinical poultry samples has been previously demonstrated. Here we demonstrate the feasibility of long read random sequencing approaches to identify disease agents in clinical samples. Experimental oropharyngeal swab samples (n = 12) from chickens infected with infectious bronchitis virus (IBV), avian influenza virus (AIV) and Mycoplasma synoviae (MS) and field-collected clinical oropharyngeal swab samples (n = 11) from Kenyan live bird markets previously testing positive for Newcastle disease virus (NDV) were randomly sequenced on the MinION platform and results validated by comparing to real time PCR and short read random sequencing in the Illumina MiSeq platform. In the swabs from experimental infections, each of three agents in every RT-qPCR-positive sample (Ct range 19–34) was detectable within 1 h on the MinION platform, except for AIV one agent in one sample (Ct = 36.21). Nine of 12 IBV-positive samples were assigned genotypes within 1 h, as were five of 11 AIV-positive samples. MinION relative abundances of the test agent (AIV, IBV and MS) were highly correlated with RT-qPCR Ct values (R range−0.82 to−0.98). In field-collected clinical swab samples, NDV (Ct range 12–37) was detected in all eleven samples within 1 h of MinION sequencing, with 10 of 11 samples accurately genotyped within 1 h. All NDV-positive field samples were found to be co-infected with one or more additional respiratory agents. These results demonstrate that MinION sequencing can provide rapid, and sensitive non-targeted detection and genetic characterization of co-existing respiratory pathogens in clinical samples with similar performance to the Illumina MiSeq. Frontiers Media S.A. 2022-12-01 /pmc/articles/PMC9751482/ /pubmed/36532355 http://dx.doi.org/10.3389/fvets.2022.1073919 Text en Copyright © 2022 Butt, Kariithi, Volkening, Taylor, Leyson, Pantin-Jackwood, Suarez, Stanton and Afonso. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Butt, Salman L.
Kariithi, Henry M.
Volkening, Jeremy D.
Taylor, Tonya L.
Leyson, Christina
Pantin-Jackwood, Mary
Suarez, David L.
Stanton, James B.
Afonso, Claudio L.
Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
title Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
title_full Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
title_fullStr Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
title_full_unstemmed Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
title_short Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
title_sort comparable outcomes from long and short read random sequencing of total rna for detection of pathogens in chicken respiratory samples
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751482/
https://www.ncbi.nlm.nih.gov/pubmed/36532355
http://dx.doi.org/10.3389/fvets.2022.1073919
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