دورية أكاديمية
أعرض في EDS

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.

التفاصيل البيبلوغرافية
العنوان: Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.
المؤلفون: Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L
مؤلفون مشاركون: EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel)
المصدر: EFSA journal. European Food Safety Authority [EFSA J] 2019 Dec 03; Vol. 17 (12), pp. e05898. Date of Electronic Publication: 2019 Dec 03 (Print Publication: 2019).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: John Wiley and Sons Ltd. Country of Publication: United States NLM ID: 101642076 Publication Model: eCollection Cited Medium: Internet ISSN: 1831-4732 (Electronic) Linking ISSN: 18314732 NLM ISO Abbreviation: EFSA J Subsets: PubMed not MEDLINE
أسماء مطبوعة: Publication: Hoboken, NJ : Parma, Italy : John Wiley and Sons Ltd. ; European Food Safety Authority
Original Publication: Parma, Italy : EFSA, [2003?]-
مستخلص: This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source-attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogen-host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS-based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.
(© 2019 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.)
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فهرسة مساهمة: Keywords: antimicrobial resistance; food‐borne outbreak investigation; metagenomics; microbial risk assessment; source attribution; typing of food‐borne pathogens; whole genome sequencing
تواريخ الأحداث: Date Created: 20200707 Latest Revision: 20240328
رمز التحديث: 20240329
مُعرف محوري في PubMed: PMC7008917
DOI: 10.2903/j.efsa.2019.5898
PMID: 32626197
قاعدة البيانات: MEDLINE
الوصف
تدمد:1831-4732
DOI:10.2903/j.efsa.2019.5898