Disclaimer

Please read before using mlstdb

Please take note of the following before using mlstdb to update your MLST databases.

Back up your databases

Always back up your original MLST databases before running any updates. This protects against accidental overwrites or deletions.

cp -r /path/to/existing/pubmlst /path/to/backup/pubmlst_backup
cp -r /path/to/existing/blast /path/to/backup/blast_backup

Curate your scheme list

Not all MLST schemes available on PubMLST and Pasteur are validated for use with the mlst tool. Before updating:

Review the scheme list if using a custom input file
Don't blindly download and apply all available schemes
Overwriting core MLST data with unverified schemes may cause downstream issues

Bacterial species only

The mlst tool is designed for typing bacterial species only. If you use the advanced fetch command to explore schemes, make sure to filter out non-bacterial schemes before updating.

Authentication requirements

Some schemes require registration with the respective database. If you encounter authentication errors during update, check that you have:

Registered with both PubMLST and Pasteur (via mlstdb connect)
Enrolled in the specific databases you need within each platform

Network considerations

mlstdb makes API calls to external servers (PubMLST and Pasteur). Be aware of:

Network interruptions — use --resume to recover
Rate limiting — keep --threads at 4 or below
Firewall restrictions — ensure outbound HTTPS access to rest.pubmlst.org and bigsdb.pasteur.fr