Submission of strain data
The Curators actively encourage the submission of any and all strain data (not just novel combinations). This is in order to make the database as representative and as useful as possible to the wider scientific community. The value of the database will depend on the quality and completeness of data entry, so please try to ensure you complete as many fields as possible.
Please note that you can only submit data on strains where all 7-alleles have been determined. If you have strain data with 6-alleles (flaA, pilE, asd, mip, mompS, proA) where you are unable to obtain neuA sequence, and which you consider to be of sufficient interest to warrant submission, please contact the curators directly. Historical 6-allele data has been retained with the aim of backfilling the missing neuA data. If you have neuA data on previously submitted strains please contact the Curators directly.
Before submitting strain data you require a SBT user ID. If you do not have one please follow the instructions on the main submission page to obtain one.
The following notes explain each of the fields on the Strain data submission form:
User ID: Enter your SBT user ID here - then use the tab button on your computer to move down the form
Email: This field will be filled automatically once the user ID is completed
Name: This field will be filled automatically once the user ID is completed
These fields are displayed so that you can be sure that your strain data will correctly be associated with your name.
ST: If known enter the ST number here
Profile: If you enter the ST number the allele numbers will be provided automatically. If you don"t have the ST select the allele number for each locus, from the dropdown menu. If you have a new allele you must submit this first using the "New allele submission" link on the main page.
Local Designation: This is the unique identifier for your strain. Please enter your designation for your strain, but please avoid using simple identifiers such as 1a, 22 etc. The idenifier should allow you to recognise your own submissions.
Source: Select from "Clinical" or "Environmental" from the dropdown menu. Although there is an "Unknown" option we would ask you not to use this option unless you really do not know. We have included this as a last resort for some reference strains where we could not determine the provenance.
From isolate or direct sample?: Select from "Isolate" or "Direct sample". By "Direct sample" we mean that no isolate was available and the SBT data were determined by direct PCR sand sequencing on a DNA extract from the clinical or environmental sample. Again, although there is an "Unknown" option we would ask you not to use this option if you can avoid it.
Investigation context: Select from "Nosocomial", "Community acquired","Travel-associated", or "Unknown".
Isolation date: Use the date format DD/MM/YYYY i.e., 2-digit number for day/2-digit number for month and 4-digit number for year. When you complete the second digit of the day the forward slash will appear automatically; similarly for the month.
Geographical information: The aim of this is to be informative and eventually to enable GIS mapping of strains, thus the more data the better! Consequently we are looking for the environmental source of the strain or if clinical where the patient obtained their infection.
Town: Should be obtainable for all environmental isolates; for clinical only use if case is nosocomial or if source has been identified or if patient did not travel away from local town during incubation period.
Region: This will vary from country to country. Please use internationally recognisable department, district, canton etc.
Country: Unless travel-associated outside country of residence should be provided
For travel-associated case only include the town/region/country where it is reasonably certain where the source of acquired infection was.
Epidemiologically related to other entries?: Select "Yes" or "No". If you select yes, please have the strain identifiers of the related strains in front of you in order that you can then select them from the list that will appear the box: "Local designations of existing entries". Select the relevant entries from this list using the mouse (left-click), to select more than 1 entry use control and left click
Relevant information: Finally, this box enables free text to be written for any extra information you consider to be relevant for your entry.
Please note any fields left blank will be filled with "Unknown" automatically but remember these missing data are of little value.
The submitter of the strain data will automatically become the contact person for their strain. This can be revealed by clicking on the EUL identifier in the results screen after querying the database.
Once you have completed your submission and clicked "Complete Submission", the contents of the form will be checked and you will be informed of any problems. If there are no problems you will be presented with a second page; this will hold a summary of the data you have submitted and if you have related this new entry to previous entries you will be asked what evidence you have to support this association. When you are happy that the data is correct, click the "Submit" button; you will receive a copy of the submission by email. The curators will check your submission and allocate a new sequence type if appropriate, then enter your data into the database.