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Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection

In a previous study, Multiplex-nanopore-sequencing based whole genome sequencing (WGS) allowed for accurate in silico serotype prediction of Salmonella within one day for five multiplexed isolates, using both SISTR and SeqSero2. Since only ten serotypes were tested in our previous study, the conclus...

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Autores principales: Wu, Xingwen, Luo, Hao, Ge, Chongtao, Xu, Feng, Deng, Xiangyu, Wiedmann, Martin, Baker, Robert C., Stevenson, Abigail E., Zhang, Guangtao, Tang, Silin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930645/
https://www.ncbi.nlm.nih.gov/pubmed/36817104
http://dx.doi.org/10.3389/fmicb.2022.1073057
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author Wu, Xingwen
Luo, Hao
Ge, Chongtao
Xu, Feng
Deng, Xiangyu
Wiedmann, Martin
Baker, Robert C.
Stevenson, Abigail E.
Zhang, Guangtao
Tang, Silin
author_facet Wu, Xingwen
Luo, Hao
Ge, Chongtao
Xu, Feng
Deng, Xiangyu
Wiedmann, Martin
Baker, Robert C.
Stevenson, Abigail E.
Zhang, Guangtao
Tang, Silin
author_sort Wu, Xingwen
collection PubMed
description In a previous study, Multiplex-nanopore-sequencing based whole genome sequencing (WGS) allowed for accurate in silico serotype prediction of Salmonella within one day for five multiplexed isolates, using both SISTR and SeqSero2. Since only ten serotypes were tested in our previous study, the conclusions above were yet to be evaluated in a larger scale test. In the current study we evaluated this workflow with 69 Salmonella serotypes and also explored the feasibility of using multiplex-nanopore-sequencing based WGS for antimicrobial resistance gene (AMR) and virulence gene detection. We found that accurate in silico serotype prediction with nanopore-WGS data was achieved within about five hours of sequencing at a minimum of 30× Salmonella genome coverage, with SeqSero2 as the serotype prediction tool. For each tested isolate, small variations were observed between the AMR/virulence gene profiles from the Illumina and Nanopore sequencing platforms. Taking results generated using Illumina data as the benchmark, the average precision value per isolate was 0.99 for both AMR and virulence gene detection. We found that the resistance gene identifier – RGI identified AMR genes with nanopore data at a much lower accuracy compared to Abricate, possibly due to RGI’s less stringent minimum similarity and coverage by default for database matching. This study is an evaluation of multiplex-nanopore-sequencing based WGS as a cost-efficient and rapid Salmonella classification method, and a starting point for future validation and verification of using it as a AMR/virulence gene profiling tool for the food industry. This study paves the way for the application of nanopore sequencing in surveillance, tracking, and risk assessment of Salmonella across the food supply chain.
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spelling pubmed-99306452023-02-16 Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection Wu, Xingwen Luo, Hao Ge, Chongtao Xu, Feng Deng, Xiangyu Wiedmann, Martin Baker, Robert C. Stevenson, Abigail E. Zhang, Guangtao Tang, Silin Front Microbiol Microbiology In a previous study, Multiplex-nanopore-sequencing based whole genome sequencing (WGS) allowed for accurate in silico serotype prediction of Salmonella within one day for five multiplexed isolates, using both SISTR and SeqSero2. Since only ten serotypes were tested in our previous study, the conclusions above were yet to be evaluated in a larger scale test. In the current study we evaluated this workflow with 69 Salmonella serotypes and also explored the feasibility of using multiplex-nanopore-sequencing based WGS for antimicrobial resistance gene (AMR) and virulence gene detection. We found that accurate in silico serotype prediction with nanopore-WGS data was achieved within about five hours of sequencing at a minimum of 30× Salmonella genome coverage, with SeqSero2 as the serotype prediction tool. For each tested isolate, small variations were observed between the AMR/virulence gene profiles from the Illumina and Nanopore sequencing platforms. Taking results generated using Illumina data as the benchmark, the average precision value per isolate was 0.99 for both AMR and virulence gene detection. We found that the resistance gene identifier – RGI identified AMR genes with nanopore data at a much lower accuracy compared to Abricate, possibly due to RGI’s less stringent minimum similarity and coverage by default for database matching. This study is an evaluation of multiplex-nanopore-sequencing based WGS as a cost-efficient and rapid Salmonella classification method, and a starting point for future validation and verification of using it as a AMR/virulence gene profiling tool for the food industry. This study paves the way for the application of nanopore sequencing in surveillance, tracking, and risk assessment of Salmonella across the food supply chain. Frontiers Media S.A. 2023-02-01 /pmc/articles/PMC9930645/ /pubmed/36817104 http://dx.doi.org/10.3389/fmicb.2022.1073057 Text en Copyright © 2023 Wu, Luo, Ge, Xu, Deng, Wiedmann, Baker, Stevenson, Zhang and Tang. 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 Microbiology
Wu, Xingwen
Luo, Hao
Ge, Chongtao
Xu, Feng
Deng, Xiangyu
Wiedmann, Martin
Baker, Robert C.
Stevenson, Abigail E.
Zhang, Guangtao
Tang, Silin
Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
title Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
title_full Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
title_fullStr Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
title_full_unstemmed Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
title_short Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
title_sort evaluation of multiplex nanopore sequencing for salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930645/
https://www.ncbi.nlm.nih.gov/pubmed/36817104
http://dx.doi.org/10.3389/fmicb.2022.1073057
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