High Throughput Sequencing for Detection of Foodborne Pathogens
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2017-10-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02029/full |
| _version_ | 1818265551127969792 |
|---|---|
| author | Camilla Sekse Arne Holst-Jensen Ulrich Dobrindt Gro S. Johannessen Weihua Li Bjørn Spilsberg Jianxin Shi |
| author_facet | Camilla Sekse Arne Holst-Jensen Ulrich Dobrindt Gro S. Johannessen Weihua Li Bjørn Spilsberg Jianxin Shi |
| author_sort | Camilla Sekse |
| collection | DOAJ |
| description | High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic “natural” strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade. |
| first_indexed | 2024-12-12T19:52:36Z |
| format | Article |
| id | doaj.art-6eeb28902b574b2aa9ca54e924f84da0 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-12T19:52:36Z |
| publishDate | 2017-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-6eeb28902b574b2aa9ca54e924f84da02022-12-22T00:13:57ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-10-01810.3389/fmicb.2017.02029270218High Throughput Sequencing for Detection of Foodborne PathogensCamilla Sekse0Arne Holst-Jensen1Ulrich Dobrindt2Gro S. Johannessen3Weihua Li4Bjørn Spilsberg5Jianxin Shi6Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, NorwayDepartment of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, NorwayInstitute of Hygiene, University of Münster, Münster, GermanyDepartment of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, NorwayJoint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaDepartment of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, NorwayJoint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaHigh-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic “natural” strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.http://journal.frontiersin.org/article/10.3389/fmicb.2017.02029/fullbacteria and virusesfungi and parasitesmetagenomicsmicrobial profilingoutbreak investigationsurveillance |
| spellingShingle | Camilla Sekse Arne Holst-Jensen Ulrich Dobrindt Gro S. Johannessen Weihua Li Bjørn Spilsberg Jianxin Shi High Throughput Sequencing for Detection of Foodborne Pathogens Frontiers in Microbiology bacteria and viruses fungi and parasites metagenomics microbial profiling outbreak investigation surveillance |
| title | High Throughput Sequencing for Detection of Foodborne Pathogens |
| title_full | High Throughput Sequencing for Detection of Foodborne Pathogens |
| title_fullStr | High Throughput Sequencing for Detection of Foodborne Pathogens |
| title_full_unstemmed | High Throughput Sequencing for Detection of Foodborne Pathogens |
| title_short | High Throughput Sequencing for Detection of Foodborne Pathogens |
| title_sort | high throughput sequencing for detection of foodborne pathogens |
| topic | bacteria and viruses fungi and parasites metagenomics microbial profiling outbreak investigation surveillance |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02029/full |
| work_keys_str_mv | AT camillasekse highthroughputsequencingfordetectionoffoodbornepathogens AT arneholstjensen highthroughputsequencingfordetectionoffoodbornepathogens AT ulrichdobrindt highthroughputsequencingfordetectionoffoodbornepathogens AT grosjohannessen highthroughputsequencingfordetectionoffoodbornepathogens AT weihuali highthroughputsequencingfordetectionoffoodbornepathogens AT bjørnspilsberg highthroughputsequencingfordetectionoffoodbornepathogens AT jianxinshi highthroughputsequencingfordetectionoffoodbornepathogens |