INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens

Ann-Katrin Llarena, Bruno Filipe Ribeiro-Gonçalves, Diogo Nuno Silva, Jani Halkilahti, Miguel Paulo Machado, Mickael Santos Da Silva, Anniina Jaakkonen, Joana Isidro, Crista Hämäläinen, Jasmin Joenperä, Vítor Borges, Luìs Viera, João Paulo Gomes, Cristina Correia, Janne Lunden, Riikka Laukkanen-Ninios, Maria Fredriksson-Ahomaa, Joseba Bikandi, Rosario San Millan, Ilargi Martinez-Ballesteros & 11 muut Lorena Laorden, Mihael Mäesaar, Lelde Grantina-Ievina, Friederike Hilbert, Javier Garaizar, Mónica Oleastro, Mari Nevas, Saara Salmenlinna, Marjaana Hakkinen, João André Carriço, Mirko Rossi

Tutkimustuotos: ArtikkelijulkaisuArtikkeliTieteellinenvertaisarvioitu

Kuvaus

Abstract In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.
Alkuperäiskielisuomi
LehtiEFSA Supporting Publications
Vuosikerta15
Numero11
Sivut1498E
Sivumäärä142
ISSN2397-8325
DOI - pysyväislinkit
TilaJulkaistu - 26 marraskuuta 2018
OKM-julkaisutyyppiA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä, vertaisarvioitu

Tieteenalat

  • 416 Elintarviketieteet
  • 1183 Kasvibiologia, mikrobiologia, virologia

Lainaa tätä

Llarena, A-K., Ribeiro-Gonçalves, B. F., Nuno Silva, D., Halkilahti, J., Machado, M. P., Da Silva, M. S., ... Rossi, M. (2018). INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens. EFSA Supporting Publications, 15(11), 1498E. https://doi.org/10.2903/sp.efsa.2018.EN-1498
Llarena, Ann-Katrin ; Ribeiro-Gonçalves, Bruno Filipe ; Nuno Silva, Diogo ; Halkilahti, Jani ; Machado, Miguel Paulo ; Da Silva, Mickael Santos ; Jaakkonen, Anniina ; Isidro, Joana ; Hämäläinen, Crista ; Joenperä, Jasmin ; Borges, Vítor ; Viera, Luìs ; Gomes, João Paulo ; Correia, Cristina ; Lunden, Janne ; Laukkanen-Ninios, Riikka ; Fredriksson-Ahomaa, Maria ; Bikandi, Joseba ; Millan, Rosario San ; Martinez-Ballesteros, Ilargi ; Laorden, Lorena ; Mäesaar, Mihael ; Grantina-Ievina, Lelde ; Hilbert, Friederike ; Garaizar, Javier ; Oleastro, Mónica ; Nevas, Mari ; Salmenlinna, Saara ; Hakkinen, Marjaana ; Carriço, João André ; Rossi, Mirko. / INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens. Julkaisussa: EFSA Supporting Publications. 2018 ; Vuosikerta 15, Nro 11. Sivut 1498E.
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title = "INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens",
abstract = "Abstract In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.",
keywords = "416 Elintarviketieteet, 1183 Kasvibiologia, mikrobiologia, virologia",
author = "Ann-Katrin Llarena and Ribeiro-Gon{\cc}alves, {Bruno Filipe} and {Nuno Silva}, Diogo and Jani Halkilahti and Machado, {Miguel Paulo} and {Da Silva}, {Mickael Santos} and Anniina Jaakkonen and Joana Isidro and Crista H{\"a}m{\"a}l{\"a}inen and Jasmin Joenper{\"a} and V{\'i}tor Borges and Lu{\`i}s Viera and Gomes, {Jo{\~a}o Paulo} and Cristina Correia and Janne Lunden and Riikka Laukkanen-Ninios and Maria Fredriksson-Ahomaa and Joseba Bikandi and Millan, {Rosario San} and Ilargi Martinez-Ballesteros and Lorena Laorden and Mihael M{\"a}esaar and Lelde Grantina-Ievina and Friederike Hilbert and Javier Garaizar and M{\'o}nica Oleastro and Mari Nevas and Saara Salmenlinna and Marjaana Hakkinen and Carri{\cc}o, {Jo{\~a}o Andr{\'e}} and Mirko Rossi",
year = "2018",
month = "11",
day = "26",
doi = "10.2903/sp.efsa.2018.EN-1498",
language = "suomi",
volume = "15",
pages = "1498E",
journal = "EFSA Supporting Publications",
issn = "2397-8325",
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Llarena, A-K, Ribeiro-Gonçalves, BF, Nuno Silva, D, Halkilahti, J, Machado, MP, Da Silva, MS, Jaakkonen, A, Isidro, J, Hämäläinen, C, Joenperä, J, Borges, V, Viera, L, Gomes, JP, Correia, C, Lunden, J, Laukkanen-Ninios, R, Fredriksson-Ahomaa, M, Bikandi, J, Millan, RS, Martinez-Ballesteros, I, Laorden, L, Mäesaar, M, Grantina-Ievina, L, Hilbert, F, Garaizar, J, Oleastro, M, Nevas, M, Salmenlinna, S, Hakkinen, M, Carriço, JA & Rossi, M 2018, 'INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens', EFSA Supporting Publications, Vuosikerta 15, Nro 11, Sivut 1498E. https://doi.org/10.2903/sp.efsa.2018.EN-1498

INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens. / Llarena, Ann-Katrin; Ribeiro-Gonçalves, Bruno Filipe; Nuno Silva, Diogo; Halkilahti, Jani; Machado, Miguel Paulo; Da Silva, Mickael Santos; Jaakkonen, Anniina; Isidro, Joana; Hämäläinen, Crista; Joenperä, Jasmin; Borges, Vítor; Viera, Luìs; Gomes, João Paulo; Correia, Cristina; Lunden, Janne; Laukkanen-Ninios, Riikka; Fredriksson-Ahomaa, Maria; Bikandi, Joseba; Millan, Rosario San; Martinez-Ballesteros, Ilargi; Laorden, Lorena; Mäesaar, Mihael; Grantina-Ievina, Lelde; Hilbert, Friederike; Garaizar, Javier; Oleastro, Mónica; Nevas, Mari; Salmenlinna, Saara; Hakkinen, Marjaana; Carriço, João André; Rossi, Mirko.

julkaisussa: EFSA Supporting Publications, Vuosikerta 15, Nro 11, 26.11.2018, s. 1498E.

Tutkimustuotos: ArtikkelijulkaisuArtikkeliTieteellinenvertaisarvioitu

TY - JOUR

T1 - INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens

AU - Llarena, Ann-Katrin

AU - Ribeiro-Gonçalves, Bruno Filipe

AU - Nuno Silva, Diogo

AU - Halkilahti, Jani

AU - Machado, Miguel Paulo

AU - Da Silva, Mickael Santos

AU - Jaakkonen, Anniina

AU - Isidro, Joana

AU - Hämäläinen, Crista

AU - Joenperä, Jasmin

AU - Borges, Vítor

AU - Viera, Luìs

AU - Gomes, João Paulo

AU - Correia, Cristina

AU - Lunden, Janne

AU - Laukkanen-Ninios, Riikka

AU - Fredriksson-Ahomaa, Maria

AU - Bikandi, Joseba

AU - Millan, Rosario San

AU - Martinez-Ballesteros, Ilargi

AU - Laorden, Lorena

AU - Mäesaar, Mihael

AU - Grantina-Ievina, Lelde

AU - Hilbert, Friederike

AU - Garaizar, Javier

AU - Oleastro, Mónica

AU - Nevas, Mari

AU - Salmenlinna, Saara

AU - Hakkinen, Marjaana

AU - Carriço, João André

AU - Rossi, Mirko

PY - 2018/11/26

Y1 - 2018/11/26

N2 - Abstract In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.

AB - Abstract In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.

KW - 416 Elintarviketieteet

KW - 1183 Kasvibiologia, mikrobiologia, virologia

U2 - 10.2903/sp.efsa.2018.EN-1498

DO - 10.2903/sp.efsa.2018.EN-1498

M3 - Artikkeli

VL - 15

SP - 1498E

JO - EFSA Supporting Publications

JF - EFSA Supporting Publications

SN - 2397-8325

IS - 11

ER -

Llarena A-K, Ribeiro-Gonçalves BF, Nuno Silva D, Halkilahti J, Machado MP, Da Silva MS et al. INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens. EFSA Supporting Publications. 2018 marras 26;15(11):1498E. https://doi.org/10.2903/sp.efsa.2018.EN-1498