Salmonella enterica
Mirko Rossi, Mickael Santos Da Silva, Bruno Filipe Ribeiro-Gonçalves, Diogo Nuno Silva, Miguel Paulo Machado, Mónica Oleastro, Vítor Borges, Joana Isidro, Luis Viera, Jani Halkilahti, Anniina Jaakkonen, Federica Palma, Saara Salmenlinna, Marjaana Hakkinen, Javier Garaizar, Joseba Bikandi, Friederike Hilbert, João André Carriço. 2018. INNUENDO whole genome and core genome MLST schemas and datasets for Salmonella enterica.(Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1323684
Escherichia coli
Mirko Rossi, Mickael Santos Da Silva, Bruno Filipe Ribeiro-Gonçalves, Diogo Nuno Silva, Miguel Paulo Machado, Mónica Oleastro, Vítor Borges, Joana Isidro, Luis Viera, Jani Halkilahti, Anniina Jaakkonen, Federica Palma, Saara Salmenlinna, Marjaana Hakkinen, Javier Garaizar, Joseba Bikandi, Friederike Hilbert, João André Carriço. 2018. INNUENDO whole genome and core genome MLST schemas and datasets for Escherichia coli. (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1323690
Campylobacter jejuni
Mirko Rossi, Mickael Santos Da Silva, Bruno Filipe Ribeiro-Gonçalves, Diogo Nuno Silva, Miguel Paulo Machado, Mónica Oleastro, Vítor Borges, Joana Isidro, Luis Viera, Dillon OR Barker, Ann-Katrin Llarena, Jani Halkilahti, Anniina Jaakkonen, Rauni Kivistö, Sara Kovanen, Timo Nieminen, Marja-Liisa Hänninen, Saara Salmenlinna, Marjaana Hakkinen, Javier Garaizar, Joseba Bikandi, Friederike Hilbert, Eduardo N Taboada, João André Carriço. 2018. INNUENDO whole genome and core genome MLST schemas and datasets for Campylobacter jejuni. (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1322564
Yersinia enterocolitica
Mirko Rossi, Mickael Santos Da Silva, Bruno Filipe Ribeiro-Gonçalves, Diogo Nuno Silva, Miguel Paulo Machado, Mónica Oleastro, Vítor Borges, Joana Isidro, Luis Viera, Jani Halkilahti, Anniina Jaakkonen, Riikka Laukkanen-Ninios, Maria Fredriksson-Ahomaa, Saara Salmenlinna, Marjaana Hakkinen, Javier Garaizar, Joseba Bikandi, Friederike Hilbert, João André Carriço. 2018. INNUENDO whole genome and core genome MLST schemas and datasets for Yersinia enterocolitica. (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1421262
The schemas are prepared to be used with chewBBACA. When using one of them with this software please cite:
Silva M, Machado M, Silva D, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço J. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. 15/03/2018. M Gen 4(3): doi:10.1099/mgen.0.000166 http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000166
Since Escherichia coli and Salmonella enterica schemas are both derived from EnteroBase wgMLST schemas, when using them please also cite:
Alikhan N-F, Zhou Z, Sergeant MJ, Achtman M (2018) A genomic overview of the population structure of Salmonella. PLoS Genet 14 (4):e1007261. https://doi.org/10.1371/journal.pgen.1007261
The isolates' genomes raw sequence data produced within the activity of the INNUENDO project were submitted to the European Nucleotide Archive (ENA) database and are publicly available under the project accession number PRJEB27020. When using the schemas, the assemblies or the allele profiles please include the project number in your publication.
The research from the INNUENDO project has received funding from European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2 (New approaches in identifying and characterizing microbial and chemical hazards) and from the Government of the Basque Country.
The conclusions, findings, and opinions expressed in this repository reflect only the view of the INNUENDO consortium members and not the official position of EFSA nor of the Government of the Basque Country. EFSA and the Government of the Basque Country are not responsible for any use that may be made of the information included in this repository. The consortium thanks all the researchers and the authorities worldwide which are contributing by submitting the raw sequences of the bacterial strains in public repositories.
The INNUENDO consortium thanks the Austrian Agency for Health and Food Safety Limited for participating in the project by providing strains of Escherichia coli, Salmonella enterica and Yersinia enterocolitica. The consortium also thanks all the researchers and the authorities worldwide which are contributing by submitting the raw sequences of the bacterial strains in ENA or SRA. The project was possible thanks to the support of CSC- Tieteen tietotekniikan keskus Oy (https://www.csc.fi/) and of INCD (http://www.incd.pt/, funded by FCT and FEDER under the project 22153-01/SAICT/2016) for providing access to cloud computing resources.
Mirko Rossi mirossilab-at-gmail.com
João André Carriço jcarrico-at-fm.ul.pt