TY - JOUR
T1 - Final report of ENGAGE - Establishing Next Generation sequencing Ability for Genomic analysis in Europe
AU - Hendriksen, Rene
AU - Karlsmose Pedersen, Susanne
AU - Leekitcharoenphon, Pimlapas
AU - Malorny, Burkhard
AU - Borowiak, Maria
AU - Battisti, Antonio
AU - Franco, Alessia
AU - Alba, Patricia
AU - Carfora, Virginia
AU - Ricci, Antonia
AU - Mastrorilli, Eleonora
AU - Losasso, Carmen
AU - Longo, Alessandra
AU - Petrin, Sara
AU - Barco, Lisa
AU - Wołkowicz, Tomasz
AU - Gierczyński, Rafal
AU - Zacharczuk, Katarzyna
AU - Wolaniuk, Natalia
AU - Wasyl, Dariusz
AU - Zajac, Magdalena
AU - Wieczorek, Kinga
AU - Pόłtorak, Katarzyna
AU - Petrovska‐Holmes, Liljana
AU - Davies, Rob
AU - Tang, Yue
AU - Grant, Kathie
AU - Underwood, Anthony
AU - Dallman, Timothy
AU - Painset, Anaïs
AU - Hartman, Hassan
AU - Al‐Shabib, Ali
AU - Cowley, Lauren
PY - 2018/6/30
Y1 - 2018/6/30
N2 - The ENGAGE project (http://www.engage-europe.eu/) was a collaboration between eight institutions across Europe. The aim was to boost the scientific cooperation to use whole genome sequencing (WGS) analysis in food safety and public health protection. ENGAGE focused on Escherichia coli (commensal E. coli) and different Salmonella spp. serotypes. A total of 3,360 genomes, 778 and 2,582 of E. coli and Salmonella, respectively, were produced. These genomes were stored and shared among partners in a temporary repository to be submitted to the European Nucleotide Archive by the end of the project. Generated genomes were used for benchmarking exercises to assess the possibility of replacing conventional typing with WGS for outbreak investigation. For the analysed strains, the benchmarking exercises showed that SPAdes assembly performed better than Velvet and that, by using different bioinformatics tools, WGS Salmonella serotyping and antimicrobial resistance genes detection, were largely in concordance with phenotypic data. Discrepancies were related to sequence quality and phenotype misclassification rather than to limitations of the bioinformatics tools. All partners were able to infer the expected phylogeny for the Salmonella and Campylobacter isolates in benchmarking exercises. Two WGS proficiency tests (assessing different genomic quality markers) were conducted among partners with satisfactory results. Guidelines including available bioinformatics tools and standard operating procedures (wet and dry lab) were prepared and posted online. Workshops, training courses and twinning programmes were conducted. The training focused on online, Galaxy-based, and command line bioinformatics tools. To reach out beyond ENGAGE, an e-learning course (17 videos) was developed and made available online. Several proof of concept projects were run and some outcomes published, e.g. the discovery of colistin resistance gene, mcr-5. Overall, the project showed that laboratories without previous WGS experience need a period of time to implement and perform WGS for foodborne pathogens routine analysis. All developed material will remain available on the ENGAGE website.
AB - The ENGAGE project (http://www.engage-europe.eu/) was a collaboration between eight institutions across Europe. The aim was to boost the scientific cooperation to use whole genome sequencing (WGS) analysis in food safety and public health protection. ENGAGE focused on Escherichia coli (commensal E. coli) and different Salmonella spp. serotypes. A total of 3,360 genomes, 778 and 2,582 of E. coli and Salmonella, respectively, were produced. These genomes were stored and shared among partners in a temporary repository to be submitted to the European Nucleotide Archive by the end of the project. Generated genomes were used for benchmarking exercises to assess the possibility of replacing conventional typing with WGS for outbreak investigation. For the analysed strains, the benchmarking exercises showed that SPAdes assembly performed better than Velvet and that, by using different bioinformatics tools, WGS Salmonella serotyping and antimicrobial resistance genes detection, were largely in concordance with phenotypic data. Discrepancies were related to sequence quality and phenotype misclassification rather than to limitations of the bioinformatics tools. All partners were able to infer the expected phylogeny for the Salmonella and Campylobacter isolates in benchmarking exercises. Two WGS proficiency tests (assessing different genomic quality markers) were conducted among partners with satisfactory results. Guidelines including available bioinformatics tools and standard operating procedures (wet and dry lab) were prepared and posted online. Workshops, training courses and twinning programmes were conducted. The training focused on online, Galaxy-based, and command line bioinformatics tools. To reach out beyond ENGAGE, an e-learning course (17 videos) was developed and made available online. Several proof of concept projects were run and some outcomes published, e.g. the discovery of colistin resistance gene, mcr-5. Overall, the project showed that laboratories without previous WGS experience need a period of time to implement and perform WGS for foodborne pathogens routine analysis. All developed material will remain available on the ENGAGE website.
U2 - 10.2903/sp.efsa.2018.EN-1431
DO - 10.2903/sp.efsa.2018.EN-1431
M3 - Article
SN - 2397-8325
VL - 15
JO - EFSA Supporting Publications
JF - EFSA Supporting Publications
IS - 6
M1 - 1431E
ER -