Unknown/ novel ST E coli

khaled mohamed

We will not accept these as new ST. Please see explanation below:

The legacy MLST website http://mlst.warwick.ac.uk, is now closed. You can no longer submit new strains with known ST designations into it. And, we no longer support new alleles and new STs based on ABI/Sanger sequencing there anymore.

During the lifespan of the legacy MLST website, one third of the new alleles we received were sequencing errors rather than real sequence variations. In addition, we don’t know how many new STs were wrong, because novel combinations of known alleles can be due to mix-ups rather than recombination. In order to improve the quality of the database, we enforce all the new allele/STs to be defined by NGS short reads. If you upload the short reads into http://enterobase.warwick.ac.uk/, we will assemble the short reads and report you back all identified allele designations. On top of this, you get access to additional information by comparing your genomes with >120,000 existing genomes from all over the world. These genomes were either published in NCBI short read archive database, or uploaded by other users.

Now the average cost for NGS sequencing of a bacterial strain has been significantly dropped. If you have difficulties in getting NGS sequencing done, we can suggest you to get in touch with https://microbesng.uk/, which gives you cheap access to NGS. On the other hand, if you still want to stay with ABI sequencing, you can download all the alleles from Enterobase and built up local MLST databases. Alternatively, you can try https://cge.cbs.dtu.dk/services/MLST/, which is an online tool for allele identifications (but will not give you new alleles).

2018-08-13T13:27:36+00:00

Comments (3)

khaled mohamed
We will not accept these as new ST. Please see explanation below:

The legacy MLST website http://mlst.warwick.ac.uk, is now closed. You can no longer submit new strains with known ST designations into it. And, we no longer support new alleles and new STs based on ABI/Sanger sequencing there anymore.

During the lifespan of the legacy MLST website, one third of the new alleles we received were sequencing errors rather than real sequence variations. In addition, we don’t know how many new STs were wrong, because novel combinations of known alleles can be due to mix-ups rather than recombination. In order to improve the quality of the database, we enforce all the new allele/STs to be defined by NGS short reads. If you upload the short reads into http://enterobase.warwick.ac.uk/, we will assemble the short reads and report you back all identified allele designations. On top of this, you get access to additional information by comparing your genomes with >120,000 existing genomes from all over the world. These genomes were either published in NCBI short read archive database, or uploaded by other users.

Now the average cost for NGS sequencing of a bacterial strain has been significantly dropped. If you have difficulties in getting NGS sequencing done, we can suggest you to get in touch with https://microbesng.uk/, which gives you cheap access to NGS. On the other hand, if you still want to stay with ABI sequencing, you can download all the alleles from Enterobase and built up local MLST databases. Alternatively, you can try https://cge.cbs.dtu.dk/services/MLST/, which is an online tool for allele identifications (but will not give you new alleles).
- 2018-08-13T13:27:36+00:00
D. R. Naveen Kumar
Thank you for the reply Khaled Mohamed.

Infact we have performed short read sequencing. My concern is that we have perfomed sequencing by Ion Torrent, not by Illumina. The database accepts only Illumina reads. Please advice how to upload Ion Torrent reads.
- 2018-09-07T08:31:46+00:00
khaled mohamed
Enterobase accept only Illumina reads
- 2018-09-08T18:43:30+00:00
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