Add Typing Results to MLST Scheme

After typing an isolate, it is possible to add the information to the MLST Scheme. There are several different possibilities when adding a typing result:

The typing result may have matched an existing sequence type completely. In this case, it is still possible and useful to add the typing result to the scheme, in order to add additional isolate metadata for the sequence type which may be from metadata annotations on the sequences or from a metadata table.

The typing result may have matched existing alleles in the scheme but in a new combination not present in any of the existing sequence types. In this case, the typing result will simply be added as a new sequence type.

The typing result may introduce new (novel) alleles to the scheme. In this case, both a new sequence type and one or more alleles are added to the scheme.

To run the Add Typing Results to MLST Scheme tool choose:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Typing and Epidemiology (Image typing_epi_folder_closed_16_h_p) | MLST Typing (Image large_mlst_open_16_h_p) | Add Typing Results to MLST Scheme (Image add_to_large_mlst_16_h_p)

Image lmlst_add_step1
Figure 12.18: Add typing result parameters.

After selecting the MLST Typing result to add, the next step is to set up the Add typing result parameters (figure 12.18):

After adding new sequence types it is necessary to recreate the Minimum Spanning Tree. The options are the same as described in the Download MLST section (Download MLST Scheme)