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Neisseria MLST News and Updates

The Neisseria meningitidis core gene list v1.0 (cgMLST) is now available. Please be aware that this current version is based only on 95% gene presence. The list therefore contains genes that could be sub-optimal for certain levels of analysis. To that end, we are working to better identify and define the paralogous loci and those loci labelled as 'hypothetical' and 'pseudogene' so that we can give a better representation of the core meningococcal genome.
Serogroup designation '29E' has been replace with 'E'. Serogroup designation 'W-135' has been replace with 'W'. This was agreed at the IPNC in 2012.
Meningitis Research Foundation (MRF) has commissioned the creation of a comprehensive online library of the genomes of all meningococcal disease isolates for 2010/11 in England, Wales and Northern Ireland, open to scientists anywhere in the world. The aim is to enable advancement in serogroup B meningococcal vaccine research, making a lasting contribution to MenB vaccine development. Genome data can be accessed from within the PubMLST database using a project-specific view.
A new clonal complex has been defined - ST-4240/6688 complex.
A new clonal complex has been defined - ST-181 complex.
Five new clonal complexes have been defined - the ST-1117, ST-1136, ST-212, ST-178 and ST-282 complexes.
PorA variable region data has been incorporated into the MLST database, enabling this serosubtyping antigen to be queried using the same interface as for MLST.
The databases are now being powered by new genomics software. This allows much greater flexibility in locus handling and has the ability to handle whole genome data.
A new clonal complex has been defined - ST-175 complex.
A penA_allele field has been added to the isolate database. This links to the penA database hosted on neisseria.org.
The isolate database has been normalized so that PubMed id values are now stored within their own table, rather than within fields in the isolate table. This means that now any number of papers can be associated with each isolate. The submission system now allows you to select a paper and submit a list of isolate id numbers that should be associated with it.
Minor changes have been made to the isolate database structure:
  • The 'strain' field has been renamed to 'isolate'.
  • A new 'strain designation' field has been created. This is a composite field, i.e. it is made up of other existing fields and does not itself exist within the database. This field is made up of serogroup, PorA variant types, FetA type, ST and clonal complex, e.g. B: P1.19,15: F5-1: ST-33 (cc32). Variant deletions are represented by 'Δ', test not done by 'ND' and data missing for other reasons, e.g. clonal complex not defined for ST, by '-'.
  • The 'strain designation' field is displayed by default in the standard results table. Consequently, the 'ST' and 'serogroup' fields are no longer displayed by default as they are redundant. You can however choose which default fields you'd like displayed by selecting them within the options page. Your choice will be remembered between sessions.
  • 'Non-groupable' has been replaced with 'NG' in the serogroup field.
Submissions to the Neisseria database should now be sent using the automated submissions system. This enables us to use a team of curators.
A new clonal complex has been defined - ST-37 complex.
An updated submission template for the isolate database is now available. An additional field has been added for the FetA variable region.
A new clonal complex has been defined - ST-4821 complex.
An updated submission template for the isolate database is now available. Additional fields have been added for antibiotic resistance breakpoints.
An updated submission template for the isolate database is now available. New allowed values have been added for source (urethral swab, joint fluid and sputum) and for disease (uncomplicated gonorrhoea and disseminated gonococcal infection). An additional field has also been added for penicillin_range which includes resistance breakpoints. Ranges for the other antibiotics will be added when the breakpoints can be agreed.
Six new clonal complexes have been defined - the ST-174, ST-103, ST-167, ST-750, ST-1157 and the ST-865 complexes.
Two new clonal complexes have been defined - ST-226 complex and ST-60 complex.
A new clonal complex has been defined - ST-461 complex.
New lactamica clonal complexes have been assigned. These are the ST-595, ST-613, ST-624, ST-640, ST-1494 and ST-1540 clonal complexes. In the database, they are clearly designated as being from lactamica, by including the species within the complex name, e.g. ST-595 complex (lactamica).
A list of recent publications that use or mention MLST in Neisseria research is now generated automatically every day, providing an overview of the latest research utilising this technique.
Website layout integrated into the pubmlst.org style.
A new clonal complex has been defined - ST-213 complex.
Advanced breakdown of isolate datasets is now available following a query. One field can be broken down by another, e.g. clonal complexes by year. You can also determine the frequencies of unique combinations of fields.
The Neisseria MLST databases are now mirrored at http://ukmirror1.pubmlst.org/neisseria/.
The ST-41 complex has been expanded to include all STs that match ST-44 at four or more loci.  The complex now has two central STs - 41 and 44, and has consequently been renamed the 'ST-41/44 complex'. A new complex has also been added - ST-162 complex.
Updated primer sequences added.
When displaying full information about an isolate following a search, if available the full citation is now displayed rather than just a PubMed id.
There is a new script available on the PubMLST (isolate) database that enables a user to query the database by cited publication.
There is a new script available on the PubMLST (isolate) database that enables a user to export full isolate information from a search as a tab-delimited text file.  These can be easily imported into spreadsheets or other analysis packages.  A new button will appear at the bottom of the isolate table when displaying data using the 'Browse database' page.
There is a new script available on the PubMLST (isolate) database that  provides a detailed breakdown of a displayed dataset.  A new link will appear at the bottom of the isolate table when displaying data using the 'Browse database' page.
The new site has gone live as part of Neisseria.org.
A drop-down listbox containing all assigned clonal complexes has been added to the query page to aid in searches by complex.
Dynamically generated pages are now cached for one day.  This should significantly speed up browsing within the site without affecting search results.  It should be possible to increase the expiry time of certain pages at a later date once the site layout has stabilised.
Allele numbers in the strain information page are now hyperlinked to provide information such as full sequence and datestamp.
The strain information page, obtained from clicking on an isolate id number in an isolate database, now makes a network connection to the PorA VR database if VR data is available.  The amino acid sequence of the variable region is returned, along with a hyperlink to the appropriate page on the PorA VR website. 
A trial server has been set up where the database has been split so that the allelic profiles and isolate data are stored separately.  This enables multiple isolate databases to be set up, all of which can connect to the profiles database (either locally or via the Internet) to query allelic profiles and allele sequences.  These isolate databases may be public or private and can represent true populations of bacteria, unlike the previous database that held data on whichever isolates were submitted.  The previous database has become the PubMLST isolate database.  Please contact the webmaster if you want further details about setting up your own isolate database that can connect to the profiles database via the Internet.
All instances of 'East Germany' and 'West Germany' have been changed to 'Germany' with a comment added concerning their original designation.  Likewise instances of 'USSR' have been changed to 'Russia'.  This was to aid data searching and has affected 12 isolates.
By request, all instances of country 'Czechoslovakia' have been changed to 'Czech Republic' to aid searching.


Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Neisseria Multi Locus Sequence Typing website (https://pubmlst.org/ neisseria/) sited at the University of Oxford (Jolley et al. Wellcome Open Res 2018, 3:124 [version 1; referees: 2 approved]). The development of this site has been funded by the Wellcome Trust and European Union.