This is the server and database for whole genomic prediction of serotypes and MLST at Department of Veterinary and Animal Sciences, University of Copenhagen. Henrik Christensen (hech@sund.ku.dk) is administrator and curator. Each species has a sequence and isolate database (links). To determine the serotype or sequence type of a sequence you should use the sequence database. Whole genomic sequencing can be provided at NGS-miseq. ____________________________________________________________________________________________________________________________________________________________ Mannheimia haemolytica for prediction of serotypes from whole genomic sequences. Use the Mannheimia haemolytica serotypes sequences link below. Select Sequence query and Best Match and upload the whole genome in FASTA format. Click Submit. The serotype is given as locus number. For serotypes 1, 2, 9 and 12 there are up to 3 alleles. They are sequence variants and are not directly related to the serotypes. Variations will be shown in case a perfect match is not obtained. This tool has been/is being developed in collaboration with Anicon Mannheimia haemolytica serotypes_sequences Mannheimia haemolytica serotypes_isolates The background and setup has been published in Christensen et al. 2021 _____________________________________________________________________________________________________________________________________________________________ Rodentibacter pneumotropicus for the prediction of 7 gene MLST (9 Dec. 2018). Rodentibacter pneumotropicus whole genome sequences Rodentibacter pneumotropicus whole genome isolates The database has been included in the paper Adhikary et al. 2019. Vet. Microbiol. 231, 11-17. The Rodentibacter pneumotropicus isolate database needs to be updated with metadata. _____________________________________________________________________________________________________________________________________________________________ Pasteurella multocida sequence database for prediction of capsule type (Carter) and LPS group. Select 'Pasteurella multocida whole genomic sequences database' and then 'sequence query', upload the genome at 'Choose file', let 'All loci' be default at 'Please select locus/scheme' and press 'Submit'. If matches to both capsular and LPS groups are not obtained, select 'CAP' for it self and repeat and then 'LPS group' for itself and repeat. The type will have a perfect match or a few mismatches. Else the strain will be non-typeable. Pasteurella multocida whole genomic sequences Pasteurella multocida whole genomic isolates LPS group 1 includes Heddleston types 1 and 14. LPS group 2 includes Heddleston types 2 and 5. LPS group 3 includes Heddleston types 3 annd 4. LPS group 4 includes Heddleston types 6 and 7. LPS group 5 includes Heddleston type 9. LPS group 6 includes Heddleston types 10, 11, 12 and 15. LPS group 7 includes Heddleston types 8 and 13. LPS group 8 includes Heddleston type 16. Capsular type prediction is based on Townsend et al. 2001 LPS group typing with prediction of Heddleston types is based on Harper et al. 2015 Further information can be found in Christensen et al. 2020. The prediction server has been described in Christensen et al. 2022. The serotype is given as locus number. The serotypes have alleles. The alleles are sequence variants and are not directly related to the serotypes. This tool has been/is being developed in collaboration with Anicon. Unpublished whole genomic sequences for setting up the database and comparison of virulence factors have been provided by Chiara Francesca Magistrali. _____________________________________________________________________________________________________________________________________________________________ fishing in river Bisenzio, Prato Status Databases for prediction of serotypes of Avibacterium paragallinarum and Riemerella anatipestifer are under construction. Citation for BIGSdb: Keith A Jolley, K. A. & Maiden, M. C. J. 2010. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11: 595