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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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1073057/full |
| _version_ | 1797937177792872448 |
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| author | Xingwen Wu Hao Luo Chongtao Ge Feng Xu Xiangyu Deng Martin Wiedmann Robert C. Baker Abigail E. Stevenson Guangtao Zhang Silin Tang |
| author_facet | Xingwen Wu Hao Luo Chongtao Ge Feng Xu Xiangyu Deng Martin Wiedmann Robert C. Baker Abigail E. Stevenson Guangtao Zhang Silin Tang |
| author_sort | Xingwen Wu |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-10T18:40:37Z |
| format | Article |
| id | doaj.art-56361d956c62443c907d2ef14ceb4f91 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-10T18:40:37Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-56361d956c62443c907d2ef14ceb4f912023-02-01T14:23:46ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-02-011310.3389/fmicb.2022.10730571073057Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detectionXingwen Wu0Hao Luo1Chongtao Ge2Feng Xu3Xiangyu Deng4Martin Wiedmann5Robert C. Baker6Abigail E. Stevenson7Guangtao Zhang8Silin Tang9Mars Global Food Safety Center, Beijing, ChinaMars Global Food Safety Center, Beijing, ChinaMars Global Food Safety Center, Beijing, ChinaMars Global Food Safety Center, Beijing, ChinaCenter for Food Safety, University of Georgia, Griffin, GA, United StatesDepartment of Food Science, Cornell University, Ithaca, NY, United StatesMars Global Food Safety Center, Beijing, ChinaMars Global Food Safety Center, Beijing, ChinaMars Global Food Safety Center, Beijing, ChinaMars Global Food Safety Center, Beijing, ChinaIn 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.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1073057/fullwhole genome sequencingOxford Nanopore TechnologiesSalmonellaserotype predictionfoodborne pathogensfood safety |
| spellingShingle | Xingwen Wu Hao Luo Chongtao Ge Feng Xu Xiangyu Deng Martin Wiedmann Robert C. Baker Abigail E. Stevenson Guangtao Zhang Silin Tang Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection Frontiers in Microbiology whole genome sequencing Oxford Nanopore Technologies Salmonella serotype prediction foodborne pathogens food safety |
| 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 | whole genome sequencing Oxford Nanopore Technologies Salmonella serotype prediction foodborne pathogens food safety |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1073057/full |
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