Submission procedure

NB. Note that the images used to illustrate the submission process are based on the Klebsiella database. However, it is important to note that the process is similar for each of the other databases. Although the specifics may vary according to the database used, the fundamental steps remain the same.

Isolates type Submission (MANDATORY)

The "isolates" submission is mandatory whether you want to define a new allele or a new MLST profile. It is used to obtain the metadata linked to the isolate(s) and also to link the new allele/MLST profile to an isolate.

NB. Note that if you have made a submission for the definition of a new MLST allele/profile but the "isolates" submission has not been made, your submission will be considered incomplete and the curators will be entitled to close it.

Once logged into the Isolates and genomes database for the pertinent bacterial group, click on "SUBMISSIONS" to access the submission panel and choose the "isolates" submission type.

Alternatively, you can access directly to the isolates type submission page for each database using the links below. Please, be sure to read the submission procedure in its entirety.

• Bordetella
• Corynebacterium diphtheriae complex
• Elizabethkingia
• Escherichia coli
• Klebsiella pneumoniae species complex
• Staphylococcus epidermidis

Please use the template provided to supply information about the isolate and the names of the assembly files. A guidance note is available in the headers of the template to help you to complete the metadata fields. Alternatively, a description of the fields for each database is available below.

• Bordetella
• Corynebacterium diphtheriae complex
• Elizabethkingia
• Escherichia coli
• Klebsiella pneumoniae species complex
• Staphylococcus epidermidis

Once you have filled in the template, please copy/paste the information into the box provided, then click "SUBMIT".

You will be redirected to a new page with a summary of the informations you have provided. Make sure everything is correct and then finalize the submission by clicking on the corresponding button.

Alleles type Submission

Once logged into the Alleles and profiles database for the pertinent bacterial group, click on "SUBMISSIONS" to access the submission panel and choose the "alleles" submission type.

You can submit any number of new sequences for a single locus and related trace files.

Before making your submission, please ensure that you have completed the steps listed below:

• Sequences should be trimmed to the correct start/end sites for the selected locus.
• Trace files should be labeled starting with the strain code (avoiding special characters such as space, dot, slash, etc.), followed by underscore, followed by the gene name written exactly as in the database (e.g. gapA), followed by underscore, followed by any information you would like, followed by .ab1 or .scf. Example: SB1_gapA_398509385_F.ab1 and SB1_gapA_398509385_R.ab1.

NB. Note that if any of the previous steps have not been followed, your submission will be considered incomplete and the curators will be entitled to close it.

NB. The discovery of a new allele is always linked to the discovery of a new MLST profile. Therefore, when submitting a new allele, it is recommended to submit the new MLST profile at the same time. This enables curators to group and process submissions more quickly.

Alternatively, you can access directly to the alleles type submission page for each database using the links below. Please, be sure to read the submission procedure in its entirety.

• Bordetella
• Corynebacterium diphtheriae complex
• Elizabethkingia
• Escherichia coli
• Klebsiella pneumoniae species complex
• Staphylococcus epidermidis

Choose the locus for which you wish to define a new allele, fill in the Sequence details fields and the sequence of your new allele.

You will be redirected to a new page for uploading trace files. For each new alleles the Sanger chromatograms (Forward & Reverse) are required.

NB. Note that you cannot upload more than 32 MB of files at a time. If you have more than 32 MB of files you will need to upload all your files in several batches of 32MB or less.

Once all the files have been uploaded, please finalize the submission by clicking on the corresponding button.

MLST Profiles type Submission

Once logged into the Alleles and profiles database for the pertinent bacterial group, click on "SUBMISSIONS" to access the submission panel and choose the "MLST profiles" submission type.

Multiple novel profiles can be provided as a single submission.

NB. Note that if all the alleles are already known in the database and only the combination of these alleles is new, the Sanger Sequencing data are not mandatory.

Alternatively, you can access directly to the MLST profiles type submission page for each database using the links below. Please, be sure to read the submission procedure in its entirety.

• Bordetella
• Corynebacterium diphtheriae complex
• Escherichia coli
• Klebsiella pneumoniae species complex

Please use the template provided to supply information about the new MLST profile. Once you've filled in the template, please copy/paste the informations into the box provided, then click on "SUBMIT".

You will be redirected to a new page with a summary of the informations you have provided. Make sure everything is correct and then finalize the submission by clicking on the corresponding button.